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IGV over X11 hprof results for version 2.1.24 and 2.3.12
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| JAVA PROFILE 1.0.1, created Fri Jul 19 08:47:09 2013 | |
| Copyright (c) 2003, 2005, Oracle and/or its affiliates. All rights reserved. | |
| Redistribution and use in source and binary forms, with or without | |
| modification, are permitted provided that the following conditions | |
| are met: | |
| - Redistributions of source code must retain the above copyright | |
| notice, this list of conditions and the following disclaimer. | |
| - Redistributions in binary form must reproduce the above copyright | |
| notice, this list of conditions and the following disclaimer in the | |
| documentation and/or other materials provided with the distribution. | |
| - Neither the name of Oracle nor the names of its | |
| contributors may be used to endorse or promote products derived | |
| from this software without specific prior written permission. | |
| THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS | |
| IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, | |
| THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR | |
| PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR | |
| CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, | |
| EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, | |
| PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR | |
| PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF | |
| LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING | |
| NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS | |
| SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. | |
| Header for -agentlib:hprof (or -Xrunhprof) ASCII Output (JDK 5.0 JVMTI based) | |
| WARNING! This file format is under development, and is subject to | |
| change without notice. | |
| This file contains the following types of records: | |
| THREAD START | |
| THREAD END mark the lifetime of Java threads | |
| TRACE represents a Java stack trace. Each trace consists | |
| of a series of stack frames. Other records refer to | |
| TRACEs to identify (1) where object allocations have | |
| taken place, (2) the frames in which GC roots were | |
| found, and (3) frequently executed methods. | |
| HEAP DUMP is a complete snapshot of all live objects in the Java | |
| heap. Following distinctions are made: | |
| ROOT root set as determined by GC | |
| CLS classes | |
| OBJ instances | |
| ARR arrays | |
| SITES is a sorted list of allocation sites. This identifies | |
| the most heavily allocated object types, and the TRACE | |
| at which those allocations occurred. | |
| CPU SAMPLES is a statistical profile of program execution. The VM | |
| periodically samples all running threads, and assigns | |
| a quantum to active TRACEs in those threads. Entries | |
| in this record are TRACEs ranked by the percentage of | |
| total quanta they consumed; top-ranked TRACEs are | |
| typically hot spots in the program. | |
| CPU TIME is a profile of program execution obtained by measuring | |
| the time spent in individual methods (excluding the time | |
| spent in callees), as well as by counting the number of | |
| times each method is called. Entries in this record are | |
| TRACEs ranked by the percentage of total CPU time. The | |
| "count" field indicates the number of times each TRACE | |
| is invoked. | |
| MONITOR TIME is a profile of monitor contention obtained by measuring | |
| the time spent by a thread waiting to enter a monitor. | |
| Entries in this record are TRACEs ranked by the percentage | |
| of total monitor contention time and a brief description | |
| of the monitor. The "count" field indicates the number of | |
| times the monitor was contended at that TRACE. | |
| MONITOR DUMP is a complete snapshot of all the monitors and threads in | |
| the System. | |
| HEAP DUMP, SITES, CPU SAMPLES|TIME and MONITOR DUMP|TIME records are generated | |
| at program exit. They can also be obtained during program execution by typing | |
| Ctrl-\ (on Solaris) or by typing Ctrl-Break (on Win32). | |
| -------- | |
| THREAD START (obj=50000139, id = 200001, name="main", group="main") | |
| THREAD START (obj=50000379, id = 200004, name="Timer-0", group="main") | |
| THREAD START (obj=50000139, id = 200005, name="Java2D Disposer", group="system") | |
| THREAD START (obj=50000139, id = 200006, name="AWT-XAWT", group="main") | |
| THREAD START (obj=50000379, id = 200007, name="process reaper", group="main") | |
| THREAD END (id = 200007) | |
| THREAD START (obj=50000379, id = 200008, name="process reaper", group="main") | |
| THREAD END (id = 200008) | |
| THREAD START (obj=50000139, id = 200009, name="Image Fetcher 0", group="main") | |
| THREAD START (obj=50000139, id = 200010, name="AWT-Shutdown", group="main") | |
| THREAD START (obj=50000898, id = 200011, name="AWT-EventQueue-0", group="main") | |
| THREAD START (obj=50000379, id = 200012, name="Timer-1", group="main") | |
| THREAD START (obj=50000139, id = 200013, name="TimerQueue", group="system") | |
| THREAD START (obj=50000139, id = 200014, name="Keep-Alive-Timer", group="system") | |
| THREAD START (obj=50000139, id = 200015, name="Thread-6", group="main") | |
| THREAD START (obj=50000139, id = 200016, name="pool-1-thread-1", group="main") | |
| THREAD END (id = 200001) | |
| THREAD START (obj=50000139, id = 200017, name="DestroyJavaVM", group="main") | |
| THREAD END (id = 200014) | |
| THREAD END (id = 200009) | |
| THREAD START (obj=50000379, id = 200019, name="Thread-1", group="main") | |
| THREAD START (obj=50000379, id = 200018, name="Thread-2", group="main") | |
| THREAD END (id = 200004) | |
| THREAD END (id = 200019) | |
| THREAD START (obj=50000139, id = 200021, name="Thread-3", group="main") | |
| THREAD END (id = 200018) | |
| THREAD START (obj=50000139, id = 200020, name="Thread-4", group="system") | |
| THREAD END (id = 200020) | |
| THREAD END (id = 200015) | |
| THREAD END (id = 200021) | |
| THREAD END (id = 200016) | |
| TRACE 300769: | |
| sun.awt.X11.XToolkit.waitForEvents(XToolkit.java:Unknown line) | |
| sun.awt.X11.XToolkit.run(XToolkit.java:568) | |
| sun.awt.X11.XToolkit.run(XToolkit.java:543) | |
| TRACE 301479: | |
| java.net.PlainSocketImpl.socketAccept(PlainSocketImpl.java:Unknown line) | |
| java.net.AbstractPlainSocketImpl.accept(AbstractPlainSocketImpl.java:375) | |
| java.net.ServerSocket.implAccept(ServerSocket.java:470) | |
| TRACE 301560: | |
| org.broad.igv.feature.ChromosomeImpl.getLength(ChromosomeImpl.java:75) | |
| org.broad.igv.feature.genome.GenomeImpl.getSequence(GenomeImpl.java:352) | |
| org.broad.igv.sam.BisulfiteCounts.incrementCounts(BisulfiteCounts.java:51) | |
| TRACE 301569: | |
| java.util.zip.Inflater.inflateBytes(Inflater.java:Unknown line) | |
| java.util.zip.Inflater.inflate(Inflater.java:255) | |
| net.sf.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:96) | |
| TRACE 301561: | |
| org.broad.igv.feature.ChromosomeImpl.getLength(ChromosomeImpl.java:75) | |
| org.broad.igv.feature.genome.GenomeImpl.getSequence(GenomeImpl.java:352) | |
| org.broad.igv.sam.BisulfiteCounts.incrementCounts(BisulfiteCounts.java:51) | |
| TRACE 301557: | |
| org.broad.igv.sam.DenseAlignmentCounts.incBlockCounts(DenseAlignmentCounts.java:331) | |
| org.broad.igv.sam.BaseAlignmentCounts.incCounts(BaseAlignmentCounts.java:95) | |
| org.broad.igv.sam.CachingQueryReader$AlignmentTile.addRecord(CachingQueryReader.java:602) | |
| TRACE 301575: | |
| net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:339) | |
| net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:269) | |
| net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:201) | |
| TRACE 301563: | |
| net.sf.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:247) | |
| java.io.DataInputStream.read(DataInputStream.java:149) | |
| net.sf.samtools.util.BinaryCodec.readBytesOrFewer(BinaryCodec.java:394) | |
| TRACE 301562: | |
| net.sf.samtools.BinaryTagCodec.readTags(BinaryTagCodec.java:303) | |
| net.sf.samtools.BAMRecord.decodeAttributes(BAMRecord.java:308) | |
| net.sf.samtools.BAMRecord.getAttribute(BAMRecord.java:288) | |
| TRACE 301573: | |
| java.lang.Integer.hashCode(Integer.java:709) | |
| java.util.HashMap.get(HashMap.java:317) | |
| org.broad.igv.sam.BisulfiteCounts.incrementCounts(BisulfiteCounts.java:92) | |
| TRACE 301510: | |
| sun.java2d.loops.DrawGlyphListAA.DrawGlyphListAA(DrawGlyphListAA.java:Unknown line) | |
| sun.java2d.pipe.AATextRenderer.drawGlyphList(AATextRenderer.java:41) | |
| sun.java2d.pipe.GlyphListPipe.drawString(GlyphListPipe.java:72) | |
| TRACE 301656: | |
| org.broad.igv.sam.BisulfiteCounts.incrementCounts(BisulfiteCounts.java:81) | |
| org.broad.igv.sam.BaseAlignmentCounts.incCounts(BaseAlignmentCounts.java:74) | |
| org.broad.igv.sam.CachingQueryReader$AlignmentTile.addRecord(CachingQueryReader.java:602) | |
| TRACE 301577: | |
| org.broad.igv.sam.SamAlignment.createAlignmentBlocks(SamAlignment.java:604) | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:150) | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) | |
| TRACE 301567: | |
| java.util.HashMap.getEntry(HashMap.java:361) | |
| java.util.HashMap.containsKey(HashMap.java:352) | |
| org.broad.igv.feature.genome.GenomeImpl.getChromosomeAlias(GenomeImpl.java:110) | |
| TRACE 301578: | |
| net.sf.samtools.util.StringUtil.bytesToString(StringUtil.java:281) | |
| net.sf.samtools.util.StringUtil.bytesToString(StringUtil.java:268) | |
| net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:205) | |
| TRACE 301586: | |
| java.lang.Integer.parseInt(Integer.java:514) | |
| org.broad.igv.sam.SamAlignment.createAlignmentBlocks(SamAlignment.java:461) | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:150) | |
| TRACE 301587: | |
| sun.java2d.x11.X11SurfaceData.XSetForeground(X11SurfaceData.java:Unknown line) | |
| sun.java2d.x11.X11SurfaceData.getGC(X11SurfaceData.java:649) | |
| sun.java2d.x11.X11SurfaceData.getRenderGC(X11SurfaceData.java:599) | |
| TRACE 301564: | |
| net.sf.samtools.BinaryCigarCodec.decode(BinaryCigarCodec.java:74) | |
| net.sf.samtools.BAMRecord.getCigar(BAMRecord.java:243) | |
| net.sf.samtools.SAMRecord.getAlignmentEnd(SAMRecord.java:456) | |
| TRACE 301566: | |
| java.util.Hashtable.get(Hashtable.java:351) | |
| org.broad.igv.PreferenceManager.getAsBoolean(PreferenceManager.java:256) | |
| org.broad.igv.sam.SamAlignment.createAlignmentBlocks(SamAlignment.java:432) | |
| TRACE 301559: | |
| java.nio.ByteBuffer.get(ByteBuffer.java:692) | |
| net.sf.samtools.BinaryTagCodec.readNullTerminatedString(BinaryTagCodec.java:417) | |
| net.sf.samtools.BinaryTagCodec.readSingleValue(BinaryTagCodec.java:318) | |
| TRACE 301639: | |
| sun.java2d.x11.X11Renderer.XDoPath(X11Renderer.java:Unknown line) | |
| sun.java2d.x11.X11Renderer.doPath(X11Renderer.java:318) | |
| sun.java2d.x11.X11Renderer.fill(X11Renderer.java:375) | |
| TRACE 301634: | |
| sun.java2d.x11.X11Renderer.XFillRect(X11Renderer.java:Unknown line) | |
| sun.java2d.x11.X11Renderer.fillRect(X11Renderer.java:211) | |
| sun.java2d.SunGraphics2D.fillRect(SunGraphics2D.java:2319) | |
| TRACE 301571: | |
| net.sf.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:374) | |
| net.sf.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:361) | |
| net.sf.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:109) | |
| TRACE 301593: | |
| org.broad.igv.sam.SamAlignment.createAlignmentBlocks(SamAlignment.java:451) | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:150) | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) | |
| TRACE 301638: | |
| sun.java2d.x11.X11Renderer.XDoPath(X11Renderer.java:Unknown line) | |
| sun.java2d.x11.X11Renderer.doPath(X11Renderer.java:318) | |
| sun.java2d.x11.X11Renderer.draw(X11Renderer.java:338) | |
| TRACE 301418: | |
| java.net.SocketInputStream.socketRead0(SocketInputStream.java:Unknown line) | |
| java.net.SocketInputStream.read(SocketInputStream.java:146) | |
| java.io.BufferedInputStream.fill(BufferedInputStream.java:235) | |
| TRACE 301534: | |
| net.sf.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:199) | |
| net.sf.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:523) | |
| net.sf.samtools.BAMFileReader$BAMFileIndexIterator.getNextRecord(BAMFileReader.java:630) | |
| TRACE 301576: | |
| java.lang.StringBuffer.append(StringBuffer.java:337) | |
| org.broad.igv.sam.SamAlignment.createAlignmentBlocks(SamAlignment.java:454) | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:150) | |
| TRACE 301554: | |
| org.broad.igv.sam.CachingQueryReader.loadTiles(CachingQueryReader.java:324) | |
| org.broad.igv.sam.CachingQueryReader.getTiles(CachingQueryReader.java:218) | |
| org.broad.igv.sam.CachingQueryReader.query(CachingQueryReader.java:140) | |
| TRACE 301556: | |
| java.io.RandomAccessFile.readBytes(RandomAccessFile.java:Unknown line) | |
| java.io.RandomAccessFile.read(RandomAccessFile.java:355) | |
| net.sf.samtools.util.SeekableFileStream.read(SeekableFileStream.java:41) | |
| TRACE 301565: | |
| java.util.ArrayList.iterator(ArrayList.java:737) | |
| net.sf.samtools.Cigar.getReferenceLength(Cigar.java:74) | |
| net.sf.samtools.SAMRecord.getAlignmentEnd(SAMRecord.java:456) | |
| TRACE 301568: | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) | |
| org.broad.igv.sam.CachingQueryReader.loadTiles(CachingQueryReader.java:276) | |
| TRACE 301580: | |
| net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:487) | |
| net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:446) | |
| net.sf.samtools.BAMFileReader$BAMQueryFilteringIterator.advance(BAMFileReader.java:715) | |
| TRACE 301665: | |
| org.broad.igv.sam.CachingQueryReader$AlignmentTile.addRecord(CachingQueryReader.java:618) | |
| org.broad.igv.sam.CachingQueryReader.loadTiles(CachingQueryReader.java:327) | |
| org.broad.igv.sam.CachingQueryReader.getTiles(CachingQueryReader.java:218) | |
| TRACE 300275: | |
| java.lang.ClassLoader.defineClass1(ClassLoader.java:Unknown line) | |
| java.lang.ClassLoader.defineClass(ClassLoader.java:634) | |
| java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142) | |
| TRACE 300772: | |
| java.io.FileInputStream.readBytes(FileInputStream.java:Unknown line) | |
| java.io.FileInputStream.read(FileInputStream.java:236) | |
| java.io.BufferedInputStream.read1(BufferedInputStream.java:273) | |
| TRACE 300773: | |
| java.lang.UNIXProcess.waitForProcessExit(UNIXProcess.java:Unknown line) | |
| java.lang.UNIXProcess.access$900(UNIXProcess.java:36) | |
| java.lang.UNIXProcess$1$1.run(UNIXProcess.java:148) | |
| TRACE 301662: | |
| java.util.ArrayList.iterator(ArrayList.java:737) | |
| org.broad.igv.sam.SamAlignment.createAlignmentBlocks(SamAlignment.java:510) | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:150) | |
| TRACE 300022: | |
| java.lang.String.intern(String.java:Unknown line) | |
| java.util.jar.Attributes$Name.<init>(Attributes.java:466) | |
| java.util.jar.Attributes.putValue(Attributes.java:168) | |
| TRACE 301328: | |
| sun.awt.X11.XlibWrapper.XSync(XlibWrapper.java:Unknown line) | |
| sun.awt.X11.XToolkit.XSync(XToolkit.java:1174) | |
| sun.awt.X11.XWM.syncTopLevelPos(XWM.java:1493) | |
| TRACE 301550: | |
| net.sf.samtools.BAMRecord.decodeBaseQualities(BAMRecord.java:317) | |
| net.sf.samtools.BAMRecord.getBaseQualities(BAMRecord.java:279) | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:150) | |
| TRACE 301631: | |
| sun.java2d.pipe.ShapeSpanIterator.setNormalize(ShapeSpanIterator.java:Unknown line) | |
| sun.java2d.pipe.ShapeSpanIterator.<init>(ShapeSpanIterator.java:77) | |
| sun.java2d.pipe.LoopPipe.getStrokeSpans(LoopPipe.java:267) | |
| TRACE 301642: | |
| sun.java2d.x11.X11Renderer.XDrawLine(X11Renderer.java:Unknown line) | |
| sun.java2d.x11.X11Renderer.drawLine(X11Renderer.java:90) | |
| sun.java2d.SunGraphics2D.drawLine(SunGraphics2D.java:2130) | |
| TRACE 301654: | |
| net.sf.samtools.SAMBinaryTagAndValue.insert(SAMBinaryTagAndValue.java:101) | |
| net.sf.samtools.SAMBinaryTagAndValue.insert(SAMBinaryTagAndValue.java:101) | |
| net.sf.samtools.BinaryTagCodec.readTags(BinaryTagCodec.java:301) | |
| TRACE 301689: | |
| java.security.AccessController.getStackAccessControlContext(AccessController.java:Unknown line) | |
| java.security.AccessController.getContext(AccessController.java:491) | |
| java.awt.AWTEvent.<init>(AWTEvent.java:109) | |
| TRACE 301699: | |
| java.lang.StringBuilder.append(StringBuilder.java:136) | |
| java.lang.StringBuilder.append(StringBuilder.java:132) | |
| net.sf.samtools.TextCigarCodec.encode(TextCigarCodec.java:61) | |
| TRACE 300020: | |
| java.lang.StringCoding$StringDecoder.decode(StringCoding.java:151) | |
| java.lang.StringCoding.decode(StringCoding.java:191) | |
| java.lang.String.<init>(String.java:451) | |
| TRACE 300100: | |
| java.util.zip.Inflater.inflateBytes(Inflater.java:Unknown line) | |
| java.util.zip.Inflater.inflate(Inflater.java:255) | |
| java.util.zip.InflaterInputStream.read(InflaterInputStream.java:152) | |
| TRACE 301533: | |
| java.lang.System.arraycopy(System.java:Unknown line) | |
| org.broad.igv.feature.genome.SequenceHelper.getSequence(SequenceHelper.java:164) | |
| org.broad.igv.feature.genome.GenomeImpl.getSequence(GenomeImpl.java:356) | |
| TRACE 301544: | |
| org.broad.igv.sam.CachingQueryReader$AlignmentTile.addRecord(CachingQueryReader.java:604) | |
| org.broad.igv.sam.CachingQueryReader.loadTiles(CachingQueryReader.java:327) | |
| org.broad.igv.sam.CachingQueryReader.getTiles(CachingQueryReader.java:218) | |
| TRACE 301545: | |
| org.broad.igv.sam.SamAlignment.setPairOrientation(SamAlignment.java:198) | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:132) | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) | |
| TRACE 301574: | |
| org.broad.igv.sam.CachingQueryReader.loadTiles(CachingQueryReader.java:310) | |
| org.broad.igv.sam.CachingQueryReader.getTiles(CachingQueryReader.java:218) | |
| org.broad.igv.sam.CachingQueryReader.query(CachingQueryReader.java:140) | |
| TRACE 301583: | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:150) | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) | |
| TRACE 301633: | |
| java.lang.StrictMath.ceil(StrictMath.java:Unknown line) | |
| java.lang.Math.ceil(Math.java:405) | |
| org.broad.igv.sam.AlignmentRenderer.drawAlignment(AlignmentRenderer.java:466) | |
| TRACE 301635: | |
| org.broad.igv.sam.AlignmentRenderer.drawAlignment(AlignmentRenderer.java:435) | |
| org.broad.igv.sam.AlignmentRenderer.renderAlignments(AlignmentRenderer.java:242) | |
| org.broad.igv.sam.AlignmentTrack.renderAlignments(AlignmentTrack.java:411) | |
| TRACE 301649: | |
| sun.misc.Unsafe.compareAndSwapInt(Unsafe.java:Unknown line) | |
| java.util.concurrent.atomic.AtomicBoolean.compareAndSet(AtomicBoolean.java:101) | |
| javax.swing.Timer.post(Timer.java:611) | |
| TRACE 301659: | |
| java.lang.StringBuilder.append(StringBuilder.java:136) | |
| org.broad.igv.feature.genome.SequenceHelper.getKey(SequenceHelper.java:208) | |
| org.broad.igv.feature.genome.SequenceHelper.getSequenceTile(SequenceHelper.java:187) | |
| TRACE 301660: | |
| org.broad.igv.sam.CachingQueryReader.loadTiles(CachingQueryReader.java:350) | |
| org.broad.igv.sam.CachingQueryReader.getTiles(CachingQueryReader.java:218) | |
| org.broad.igv.sam.CachingQueryReader.query(CachingQueryReader.java:140) | |
| TRACE 301670: | |
| java.util.HashMap.get(HashMap.java:317) | |
| org.broad.igv.sam.AlignmentTrack.getBisulfiteContextPostContext(AlignmentTrack.java:749) | |
| org.broad.igv.sam.BisulfiteCounts.contextIsMatching(BisulfiteCounts.java:144) | |
| TRACE 301691: | |
| java.util.Collections$UnmodifiableCollection$1.<init>(Collections.java:1023) | |
| java.util.Collections$UnmodifiableCollection.iterator(Collections.java:1022) | |
| net.sf.samtools.TextCigarCodec.encode(TextCigarCodec.java:59) | |
| TRACE 301693: | |
| net.sf.samtools.SAMReadGroupRecord.getPlatform(SAMReadGroupRecord.java:75) | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:141) | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) | |
| TRACE 301705: | |
| net.sf.samtools.util.StringUtil.bytesToString(StringUtil.java:281) | |
| net.sf.samtools.BAMRecord.decodeReadName(BAMRecord.java:331) | |
| net.sf.samtools.BAMRecord.getReadName(BAMRecord.java:220) | |
| TRACE 301706: | |
| net.sf.samtools.util.StringUtil.bytesToString(StringUtil.java:281) | |
| net.sf.samtools.util.StringUtil.bytesToString(StringUtil.java:268) | |
| net.sf.samtools.BinaryTagCodec.readNullTerminatedString(BinaryTagCodec.java:420) | |
| TRACE 300257: | |
| sun.security.provider.DigestBase.engineUpdate(DigestBase.java:139) | |
| java.security.MessageDigest$Delegate.engineUpdate(MessageDigest.java:555) | |
| java.security.MessageDigest.update(MessageDigest.java:300) | |
| TRACE 300260: | |
| java.util.HashMap$HashIterator.nextEntry(HashMap.java:809) | |
| java.util.HashMap$EntryIterator.next(HashMap.java:851) | |
| java.util.HashMap$EntryIterator.next(HashMap.java:849) | |
| TRACE 301352: | |
| sun.awt.X11.XlibWrapper.XQueryTree(XlibWrapper.java:Unknown line) | |
| sun.awt.X11.XQueryTree.execute(XQueryTree.java:68) | |
| sun.awt.X11.XQueryTree.execute(XQueryTree.java:52) | |
| TRACE 301419: | |
| sun.awt.X11.XlibWrapper.XGetWindowAttributes(XlibWrapper.java:Unknown line) | |
| sun.awt.X11.XWM.syncTopLevelPos(XWM.java:1488) | |
| sun.awt.X11.XWM.getInsets(XWM.java:1599) | |
| TRACE 301513: | |
| java.security.AccessController.doPrivileged(AccessController.java:Unknown line) | |
| java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:105) | |
| java.awt.EventQueue.dispatchEvent(EventQueue.java:617) | |
| TRACE 301529: | |
| org.broad.igv.sam.SamAlignment.createAlignmentBlocks(SamAlignment.java:486) | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:150) | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) | |
| TRACE 301540: | |
| net.sf.samtools.BAMRecord.decodeBaseQualities(BAMRecord.java:313) | |
| net.sf.samtools.BAMRecord.getBaseQualities(BAMRecord.java:279) | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:150) | |
| TRACE 301579: | |
| net.sf.samtools.SAMBinaryTagAndValue.find(SAMBinaryTagAndValue.java:119) | |
| net.sf.samtools.SAMRecord.getAttribute(SAMRecord.java:1083) | |
| net.sf.samtools.BAMRecord.getAttribute(BAMRecord.java:290) | |
| TRACE 301581: | |
| net.sf.samtools.SAMRecord.getCigarString(SAMRecord.java:580) | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:119) | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) | |
| TRACE 301582: | |
| org.broad.igv.sam.CachingQueryReader$AlignmentTile.addRecord(CachingQueryReader.java:602) | |
| org.broad.igv.sam.CachingQueryReader.loadTiles(CachingQueryReader.java:327) | |
| org.broad.igv.sam.CachingQueryReader.getTiles(CachingQueryReader.java:218) | |
| TRACE 301588: | |
| net.sf.samtools.SAMReadGroupRecord.getKeySequence(SAMReadGroupRecord.java:87) | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:145) | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) | |
| TRACE 301589: | |
| java.lang.Object.clone(Object.java:Unknown line) | |
| sun.java2d.SunGraphics2D.clone(SunGraphics2D.java:265) | |
| sun.java2d.SunGraphics2D.create(SunGraphics2D.java:299) | |
| TRACE 301591: | |
| java.util.Hashtable.get(Hashtable.java:354) | |
| org.broad.igv.PreferenceManager.getAsBoolean(PreferenceManager.java:256) | |
| org.broad.igv.sam.SamAlignment.createAlignmentBlocks(SamAlignment.java:432) | |
| TRACE 301592: | |
| org.broad.igv.sam.BaseAlignmentCounts.incCounts(BaseAlignmentCounts.java:74) | |
| org.broad.igv.sam.CachingQueryReader$AlignmentTile.addRecord(CachingQueryReader.java:602) | |
| org.broad.igv.sam.CachingQueryReader.loadTiles(CachingQueryReader.java:327) | |
| TRACE 301598: | |
| java.util.Arrays.mergeSort(Arrays.java:1306) | |
| java.util.Arrays.mergeSort(Arrays.java:1295) | |
| java.util.Arrays.mergeSort(Arrays.java:1294) | |
| TRACE 301637: | |
| sun.java2d.pisces.Stroker.<init>(Stroker.java:79) | |
| sun.java2d.pisces.PiscesRenderingEngine.strokeTo(PiscesRenderingEngine.java:347) | |
| sun.java2d.pisces.PiscesRenderingEngine.strokeTo(PiscesRenderingEngine.java:164) | |
| TRACE 301647: | |
| sun.java2d.loops.MaskBlit.MaskBlit(MaskBlit.java:Unknown line) | |
| sun.java2d.loops.Blit$GeneralMaskBlit.Blit(Blit.java:204) | |
| sun.java2d.pipe.DrawImage.blitSurfaceData(DrawImage.java:956) | |
| TRACE 301671: | |
| net.sf.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:193) | |
| net.sf.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:523) | |
| net.sf.samtools.BAMFileReader$BAMFileIndexIterator.getNextRecord(BAMFileReader.java:630) | |
| TRACE 301674: | |
| net.sf.samtools.Cigar.isEmpty(Cigar.java:66) | |
| net.sf.samtools.TextCigarCodec.encode(TextCigarCodec.java:55) | |
| net.sf.samtools.SAMRecord.getCigarString(SAMRecord.java:580) | |
| TRACE 301675: | |
| sun.font.X11TextRenderer.doDrawGlyphList(X11TextRenderer.java:Unknown line) | |
| sun.font.X11TextRenderer.drawGlyphList(X11TextRenderer.java:80) | |
| sun.java2d.pipe.GlyphListPipe.drawString(GlyphListPipe.java:72) | |
| TRACE 301677: | |
| java.util.HashMap.get(HashMap.java:317) | |
| org.broad.igv.sam.AlignmentTrack.getBisulfiteContextPreContext(AlignmentTrack.java:744) | |
| org.broad.igv.sam.BisulfiteCounts.contextIsMatching(BisulfiteCounts.java:143) | |
| TRACE 301687: | |
| java.security.AccessController.doPrivileged(AccessController.java:Unknown line) | |
| javax.swing.Timer.post(Timer.java:612) | |
| javax.swing.TimerQueue.run(TimerQueue.java:177) | |
| TRACE 301692: | |
| java.awt.Component.getGraphicsConfiguration(Component.java:1029) | |
| javax.swing.RepaintManager.getVolatileOffscreenBuffer(RepaintManager.java:963) | |
| javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1370) | |
| TRACE 301697: | |
| org.broad.igv.feature.ChromosomeImpl.getLength(ChromosomeImpl.java:75) | |
| org.broad.igv.feature.genome.GenomeImpl.getSequence(GenomeImpl.java:356) | |
| org.broad.igv.sam.BisulfiteCounts.incrementCounts(BisulfiteCounts.java:51) | |
| TRACE 300001: | |
| java.lang.ClassLoader.findBootstrapClass(ClassLoader.java:Unknown line) | |
| java.lang.ClassLoader.findBootstrapClass0(ClassLoader.java:900) | |
| java.lang.ClassLoader.loadClass(ClassLoader.java:316) | |
| TRACE 300016: | |
| java.util.jar.Manifest.read(Manifest.java:229) | |
| java.util.jar.Manifest.<init>(Manifest.java:69) | |
| java.util.jar.JarFile.getManifestFromReference(JarFile.java:177) | |
| TRACE 300017: | |
| java.lang.String.<init>(String.java:347) | |
| java.util.jar.Attributes.read(Attributes.java:412) | |
| java.util.jar.Manifest.read(Manifest.java:251) | |
| TRACE 300018: | |
| java.util.HashMap.<init>(HashMap.java:204) | |
| java.util.HashMap.<init>(HashMap.java:216) | |
| java.util.jar.Attributes.<init>(Attributes.java:74) | |
| TRACE 300019: | |
| java.util.jar.Attributes.read(Attributes.java:372) | |
| java.util.jar.Manifest.read(Manifest.java:251) | |
| java.util.jar.Manifest.<init>(Manifest.java:69) | |
| TRACE 300033: | |
| sun.misc.URLClassPath$JarLoader.checkResource(URLClassPath.java:701) | |
| sun.misc.URLClassPath$JarLoader.getResource(URLClassPath.java:773) | |
| sun.misc.URLClassPath.getResource(URLClassPath.java:185) | |
| TRACE 300105: | |
| java.util.Arrays.copyOfRange(Arrays.java:3221) | |
| java.lang.String.<init>(String.java:233) | |
| java.lang.StringBuilder.toString(StringBuilder.java:447) | |
| TRACE 300106: | |
| java.lang.AbstractStringBuilder.<init>(AbstractStringBuilder.java:62) | |
| java.lang.StringBuilder.<init>(StringBuilder.java:85) | |
| sun.security.util.ManifestDigester.<init>(ManifestDigester.java:132) | |
| TRACE 300151: | |
| sun.security.x509.RDN.<init>(RDN.java:247) | |
| sun.security.x509.X500Name.parseDER(X500Name.java:804) | |
| sun.security.x509.X500Name.<init>(X500Name.java:307) | |
| TRACE 300232: | |
| java.io.BufferedInputStream.read(BufferedInputStream.java:258) | |
| java.io.DataInputStream.readChar(DataInputStream.java:362) | |
| sun.text.normalizer.NormalizerDataReader.read(NormalizerDataReader.java:340) | |
| TRACE 300250: | |
| sun.security.provider.SHA.implCompress(SHA.java:161) | |
| sun.security.provider.DigestBase.engineUpdate(DigestBase.java:139) | |
| java.security.MessageDigest$Delegate.engineUpdate(MessageDigest.java:555) | |
| TRACE 300251: | |
| sun.misc.Unsafe.getInt(Unsafe.java:Unknown line) | |
| sun.security.provider.ByteArrayAccess.b2iBig64(ByteArrayAccess.java:263) | |
| sun.security.provider.SHA.implCompress(SHA.java:122) | |
| TRACE 300276: | |
| org.broad.igv.ui.Main.<clinit>(Main.java:56) | |
| TRACE 300297: | |
| java.util.HashMap.createEntry(HashMap.java:784) | |
| java.util.HashMap.putForCreate(HashMap.java:447) | |
| java.util.HashMap.putAllForCreate(HashMap.java:453) | |
| TRACE 300298: | |
| sun.security.util.ManifestDigester.<init>(ManifestDigester.java:178) | |
| java.util.jar.JarVerifier.processEntry(JarVerifier.java:267) | |
| java.util.jar.JarVerifier.update(JarVerifier.java:205) | |
| TRACE 300299: | |
| java.lang.Throwable.fillInStackTrace(Throwable.java:Unknown line) | |
| java.lang.Throwable.<init>(Throwable.java:198) | |
| java.lang.Exception.<init>(Exception.java:46) | |
| TRACE 300355: | |
| sun.util.resources.LocaleData$1.run(LocaleData.java:142) | |
| java.security.AccessController.doPrivileged(AccessController.java:Unknown line) | |
| sun.util.resources.LocaleData.getBundle(LocaleData.java:140) | |
| TRACE 300420: | |
| com.sun.org.apache.xerces.internal.parsers.XML11Configuration.<init>(XML11Configuration.java:533) | |
| com.sun.org.apache.xerces.internal.parsers.XIncludeAwareParserConfiguration.<init>(XIncludeAwareParserConfiguration.java:128) | |
| com.sun.org.apache.xerces.internal.parsers.XIncludeAwareParserConfiguration.<init>(XIncludeAwareParserConfiguration.java:89) | |
| TRACE 300482: | |
| com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.doctypeDecl(XMLDTDValidator.java:758) | |
| com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.scanDoctypeDecl(XMLDocumentScannerImpl.java:689) | |
| com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(XMLDocumentScannerImpl.java:945) | |
| TRACE 300530: | |
| javax.swing.filechooser.FileSystemView.getFileSystemView(FileSystemView.java:80) | |
| org.broad.igv.DirectoryManager.getUserDirectory(DirectoryManager.java:59) | |
| org.broad.igv.ui.Main.initApplication(Main.java:78) | |
| TRACE 300572: | |
| sun.awt.X11GraphicsEnvironment.initDisplay(X11GraphicsEnvironment.java:Unknown line) | |
| sun.awt.X11GraphicsEnvironment.access$200(X11GraphicsEnvironment.java:62) | |
| sun.awt.X11GraphicsEnvironment$1.run(X11GraphicsEnvironment.java:178) | |
| TRACE 300592: | |
| java.lang.Class.forName0(Class.java:Unknown line) | |
| java.lang.Class.forName(Class.java:186) | |
| java.awt.Toolkit$2.run(Toolkit.java:849) | |
| TRACE 300622: | |
| java.lang.String.equals(String.java:1025) | |
| java.util.Vector.indexOf(Vector.java:381) | |
| java.util.Vector.contains(Vector.java:340) | |
| TRACE 300667: | |
| sun.java2d.NullSurfaceData.<init>(NullSurfaceData.java:46) | |
| sun.java2d.NullSurfaceData.<clinit>(NullSurfaceData.java:43) | |
| sun.java2d.SurfaceData.initIDs(SurfaceData.java:Unknown line) | |
| TRACE 300740: | |
| sun.awt.X11.XToolkit.keysymToPrimaryKeycode(XToolkit.java:1542) | |
| sun.awt.X11.XToolkit.setupModifierMap(XToolkit.java:1560) | |
| sun.awt.X11.XToolkit.<clinit>(XToolkit.java:119) | |
| TRACE 300770: | |
| java.lang.UNIXProcess$1$1.run(UNIXProcess.java:125) | |
| TRACE 300794: | |
| java.awt.KeyboardFocusManager.<init>(KeyboardFocusManager.java:287) | |
| java.awt.DefaultKeyboardFocusManager.<init>(DefaultKeyboardFocusManager.java:64) | |
| java.awt.KeyboardFocusManager.getCurrentKeyboardFocusManager(KeyboardFocusManager.java:190) | |
| TRACE 300831: | |
| javax.swing.LookAndFeel.installProperty(LookAndFeel.java:274) | |
| javax.swing.plaf.basic.BasicPanelUI.installDefaults(BasicPanelUI.java:71) | |
| javax.swing.plaf.basic.BasicPanelUI.installUI(BasicPanelUI.java:56) | |
| TRACE 300853: | |
| java.lang.String.toUpperCase(String.java:2588) | |
| sun.security.util.ManifestEntryVerifier.setEntry(ManifestEntryVerifier.java:120) | |
| java.util.jar.JarVerifier.beginEntry(JarVerifier.java:162) | |
| TRACE 300858: | |
| java.util.HashMap$HashIterator.<init>(HashMap.java:796) | |
| java.util.HashMap$EntryIterator.<init>(HashMap.java:849) | |
| java.util.HashMap$EntryIterator.<init>(HashMap.java:849) | |
| TRACE 300924: | |
| java.io.RandomAccessFile.seek(RandomAccessFile.java:Unknown line) | |
| javax.imageio.stream.FileCacheImageInputStream.read(FileCacheImageInputStream.java:188) | |
| javax.imageio.stream.ImageInputStreamImpl.readShort(ImageInputStreamImpl.java:228) | |
| TRACE 300935: | |
| java.lang.StrictMath.floor(StrictMath.java:Unknown line) | |
| java.lang.Math.floor(Math.java:424) | |
| java.lang.Math.round(Math.java:652) | |
| TRACE 300948: | |
| com.sun.imageio.plugins.gif.GIFImageReader.initializeStringTable(GIFImageReader.java:351) | |
| com.sun.imageio.plugins.gif.GIFImageReader.read(GIFImageReader.java:929) | |
| javax.imageio.ImageIO.read(ImageIO.java:1438) | |
| TRACE 300949: | |
| java.lang.String.concat(String.java:2012) | |
| java.lang.Package.getSystemPackage(Package.java:512) | |
| java.lang.ClassLoader.getPackage(ClassLoader.java:1447) | |
| TRACE 300969: | |
| org.broad.igv.session.Session.<init>(Session.java:49) | |
| org.broad.igv.ui.IGV.<init>(IGV.java:220) | |
| org.broad.igv.ui.IGV.createInstance(IGV.java:142) | |
| TRACE 300991: | |
| java.util.Vector.removeElementAt(Vector.java:543) | |
| java.util.Vector.removeElement(Vector.java:616) | |
| sun.awt.image.ImageFetcher.nextImage(ImageFetcher.java:140) | |
| TRACE 301004: | |
| sun.awt.X11.XlibWrapper.XQueryBestCursor(XlibWrapper.java:Unknown line) | |
| sun.awt.X11.XCustomCursor.getBestCursorSize(XCustomCursor.java:63) | |
| sun.awt.X11.XToolkit.getBestCursorSize(XToolkit.java:1080) | |
| TRACE 301008: | |
| javax.swing.JComboBox.installAncestorListener(JComboBox.java:231) | |
| javax.swing.JComboBox.init(JComboBox.java:225) | |
| javax.swing.JComboBox.<init>(JComboBox.java:221) | |
| TRACE 301055: | |
| sun.awt.X11.XlibWrapper.InternAtom(XlibWrapper.java:Unknown line) | |
| sun.awt.X11.XAtom.<init>(XAtom.java:271) | |
| sun.awt.X11.XAtom.<init>(XAtom.java:236) | |
| TRACE 301095: | |
| javax.swing.plaf.basic.BasicComboBoxEditor.createEditorComponent(BasicComboBoxEditor.java:65) | |
| javax.swing.plaf.basic.BasicComboBoxEditor.<init>(BasicComboBoxEditor.java:50) | |
| javax.swing.plaf.metal.MetalComboBoxEditor.<init>(MetalComboBoxEditor.java:53) | |
| TRACE 301184: | |
| javax.swing.plaf.metal.MetalComboBoxUI.createArrowButton(MetalComboBoxUI.java:171) | |
| javax.swing.plaf.basic.BasicComboBoxUI.installComponents(BasicComboBoxUI.java:691) | |
| javax.swing.plaf.basic.BasicComboBoxUI.installUI(BasicComboBoxUI.java:266) | |
| TRACE 301189: | |
| java.util.zip.ZipFile.getEntry(ZipFile.java:Unknown line) | |
| java.util.zip.ZipFile.getEntry(ZipFile.java:166) | |
| java.util.jar.JarFile.getEntry(JarFile.java:223) | |
| TRACE 301190: | |
| javax.swing.ArrayTable.put(ArrayTable.java:110) | |
| javax.swing.InputMap.put(InputMap.java:103) | |
| javax.swing.LookAndFeel.loadKeyBindings(LookAndFeel.java:437) | |
| TRACE 301196: | |
| sun.security.util.ManifestEntryVerifier.setEntry(ManifestEntryVerifier.java:120) | |
| java.util.jar.JarVerifier.beginEntry(JarVerifier.java:162) | |
| java.util.jar.JarVerifier$VerifierStream.<init>(JarVerifier.java:398) | |
| TRACE 301197: | |
| java.util.Collections.synchronizedList(Collections.java:1794) | |
| org.broad.igv.track.TrackGroup.<init>(TrackGroup.java:63) | |
| org.broad.igv.track.TrackGroup.<init>(TrackGroup.java:57) | |
| TRACE 301198: | |
| java.awt.Component.repaint(Component.java:3074) | |
| javax.swing.JComponent.setFont(JComponent.java:2727) | |
| javax.swing.LookAndFeel.installColorsAndFont(LookAndFeel.java:207) | |
| TRACE 301204: | |
| org.broad.igv.ui.util.MenuAndToolbarUtils.createMenuItem(MenuAndToolbarUtils.java:60) | |
| org.broad.igv.ui.IGVMenuBar.createFileMenu(IGVMenuBar.java:109) | |
| org.broad.igv.ui.IGVMenuBar.createMenus(IGVMenuBar.java:78) | |
| TRACE 301219: | |
| javax.swing.DefaultButtonModel.addChangeListener(DefaultButtonModel.java:305) | |
| javax.swing.AbstractButton.setModel(AbstractButton.java:1754) | |
| javax.swing.JMenuItem.setModel(JMenuItem.java:172) | |
| TRACE 301224: | |
| javax.swing.UIManager.maybeInitialize(UIManager.java:1393) | |
| javax.swing.UIManager.getDefaults(UIManager.java:644) | |
| javax.swing.UIManager.getColor(UIManager.java:686) | |
| TRACE 301244: | |
| java.util.Arrays.binarySearch0(Arrays.java:2106) | |
| java.util.Arrays.binarySearch(Arrays.java:2046) | |
| sun.java2d.loops.GraphicsPrimitiveMgr.locate(GraphicsPrimitiveMgr.java:242) | |
| TRACE 301245: | |
| sun.awt.X11.XEvent.get_xany(XEvent.java:42) | |
| sun.awt.X11.XToolkit.run(XToolkit.java:588) | |
| sun.awt.X11.XToolkit.run(XToolkit.java:543) | |
| TRACE 301284: | |
| sun.awt.X11.XDragAndDropProtocols.<clinit>(XDragAndDropProtocols.java:62) | |
| sun.awt.X11.XDropTargetRegistry.registerDropSite(XDropTargetRegistry.java:566) | |
| sun.awt.X11.XWindowPeer.addDropTarget(XWindowPeer.java:1831) | |
| TRACE 301308: | |
| sun.nio.cs.UTF_16.newDecoder(UTF_16.java:44) | |
| java.lang.StringCoding$StringDecoder.<init>(StringCoding.java:134) | |
| java.lang.StringCoding$StringDecoder.<init>(StringCoding.java:126) | |
| TRACE 301330: | |
| java.lang.String.endsWith(String.java:1477) | |
| sun.security.util.ManifestEntryVerifier.setEntry(ManifestEntryVerifier.java:120) | |
| java.util.jar.JarVerifier.beginEntry(JarVerifier.java:162) | |
| TRACE 301331: | |
| java.awt.Container.minimumSize(Container.java:1657) | |
| java.awt.Container.getMinimumSize(Container.java:1642) | |
| javax.swing.JComponent.getMinimumSize(JComponent.java:1716) | |
| TRACE 301406: | |
| java.net.Inet6AddressImpl.lookupAllHostAddr(Inet6AddressImpl.java:Unknown line) | |
| java.net.InetAddress$1.lookupAllHostAddr(InetAddress.java:867) | |
| java.net.InetAddress.getAddressFromNameService(InetAddress.java:1246) | |
| TRACE 301432: | |
| sun.awt.X11.XlibWrapper.XEventsQueued(XlibWrapper.java:Unknown line) | |
| sun.awt.X11.XToolkit.run(XToolkit.java:565) | |
| sun.awt.X11.XToolkit.run(XToolkit.java:543) | |
| TRACE 301433: | |
| java.awt.Container.paint(Container.java:1784) | |
| javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:794) | |
| javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:735) | |
| TRACE 301447: | |
| sun.awt.X11.XInputMethod.openXIMNative(XInputMethod.java:Unknown line) | |
| sun.awt.X11.XInputMethod.openXIM(XInputMethod.java:62) | |
| sun.awt.X11InputMethod.initXIM(X11InputMethod.java:202) | |
| TRACE 301448: | |
| sun.awt.im.InputContext.focusGained(InputContext.java:300) | |
| sun.awt.im.InputContext.dispatchEvent(InputContext.java:244) | |
| sun.awt.im.InputMethodContext.dispatchEvent(InputMethodContext.java:197) | |
| TRACE 301461: | |
| java.awt.Container.addImpl(Container.java:1030) | |
| javax.swing.CellRendererPane.addImpl(CellRendererPane.java:106) | |
| java.awt.Container.add(Container.java:373) | |
| TRACE 301462: | |
| java.util.ArrayList.add(ArrayList.java:378) | |
| java.util.regex.Pattern.split(Pattern.java:1020) | |
| java.util.regex.Pattern.split(Pattern.java:1076) | |
| TRACE 301470: | |
| org.broad.igv.ui.panel.ReferenceFrame.setChromosomeName(ReferenceFrame.java:422) | |
| org.broad.igv.ui.panel.ReferenceFrame.setChromosomeName(ReferenceFrame.java:432) | |
| org.broad.igv.ui.IGVCommandBar$14.run(IGVCommandBar.java:1021) | |
| TRACE 301471: | |
| java.lang.Thread.currentThread(Thread.java:Unknown line) | |
| java.util.concurrent.locks.ReentrantLock$Sync.tryRelease(ReentrantLock.java:154) | |
| java.util.concurrent.locks.AbstractQueuedSynchronizer.release(AbstractQueuedSynchronizer.java:1262) | |
| TRACE 301478: | |
| sun.swing.CachedPainter.getCache(CachedPainter.java:64) | |
| sun.swing.CachedPainter.<init>(CachedPainter.java:78) | |
| javax.swing.plaf.metal.MetalUtils$GradientPainter.<init>(MetalUtils.java:250) | |
| TRACE 301492: | |
| sun.awt.X11.XlibWrapper.XSync(XlibWrapper.java:Unknown line) | |
| sun.awt.X11.XToolkit.XSync(XToolkit.java:1174) | |
| sun.awt.X11.XWM.setLayer(XWM.java:1199) | |
| TRACE 301504: | |
| javax.swing.plaf.metal.MetalComboBoxIcon.paintIcon(MetalComboBoxIcon.java:50) | |
| javax.swing.plaf.metal.MetalComboBoxButton.paintComponent(MetalComboBoxButton.java:153) | |
| javax.swing.JComponent.paint(JComponent.java:1029) | |
| TRACE 301505: | |
| java.awt.Component.getParent(Component.java:929) | |
| javax.swing.LayoutComparator.compare(LayoutComparator.java:70) | |
| java.util.Arrays.mergeSort(Arrays.java:1306) | |
| TRACE 301506: | |
| java.lang.String.concat(String.java:2012) | |
| java.net.URLClassLoader$1.run(URLClassLoader.java:208) | |
| java.security.AccessController.doPrivileged(AccessController.java:Unknown line) | |
| TRACE 301507: | |
| sun.misc.Unsafe.getFloat(Unsafe.java:Unknown line) | |
| sun.font.FileFontStrike.getGlyphMetrics(FileFontStrike.java:642) | |
| sun.font.CompositeStrike.getGlyphMetrics(CompositeStrike.java:138) | |
| TRACE 301508: | |
| sun.java2d.loops.MaskBlit.MaskBlit(MaskBlit.java:Unknown line) | |
| sun.java2d.loops.Blit$GeneralMaskBlit.Blit(Blit.java:204) | |
| sun.java2d.pipe.AlphaPaintPipe.renderPathTile(AlphaPaintPipe.java:156) | |
| TRACE 301509: | |
| java.security.AccessController.getStackAccessControlContext(AccessController.java:Unknown line) | |
| java.security.AccessController.getContext(AccessController.java:491) | |
| java.awt.EventQueue.dispatchEvent(EventQueue.java:613) | |
| TRACE 301511: | |
| sun.misc.Unsafe.unpark(Unsafe.java:Unknown line) | |
| java.util.concurrent.locks.LockSupport.unpark(LockSupport.java:152) | |
| java.util.concurrent.locks.AbstractQueuedSynchronizer.unparkSuccessor(AbstractQueuedSynchronizer.java:666) | |
| TRACE 301512: | |
| java.awt.EventQueue.getNextEvent(EventQueue.java:486) | |
| java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:247) | |
| java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:200) | |
| TRACE 301522: | |
| java.security.MessageDigest$Delegate.engineUpdate(MessageDigest.java:556) | |
| java.security.MessageDigest.update(MessageDigest.java:300) | |
| sun.security.util.ManifestEntryVerifier.update(ManifestEntryVerifier.java:166) | |
| TRACE 301526: | |
| java.lang.Object.hashCode(Object.java:Unknown line) | |
| java.lang.Enum.hashCode(Enum.java:139) | |
| java.util.HashMap.get(HashMap.java:317) | |
| TRACE 301527: | |
| java.util.HashMap.getEntry(HashMap.java:361) | |
| java.util.HashMap.containsKey(HashMap.java:352) | |
| org.broad.igv.feature.genome.GenomeImpl.getChromosomeAlias(GenomeImpl.java:110) | |
| TRACE 301528: | |
| java.lang.System.arraycopy(System.java:Unknown line) | |
| net.sf.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:243) | |
| java.io.DataInputStream.read(DataInputStream.java:149) | |
| TRACE 301530: | |
| org.broad.igv.sam.SamAlignment.createAlignmentBlocks(SamAlignment.java:481) | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:150) | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) | |
| TRACE 301531: | |
| java.nio.Buffer.flip(Buffer.java:348) | |
| net.sf.samtools.util.BinaryCodec.readUShort(BinaryCodec.java:562) | |
| net.sf.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:194) | |
| TRACE 301532: | |
| java.util.ArrayList.<init>(ArrayList.java:132) | |
| java.util.ArrayList.<init>(ArrayList.java:139) | |
| net.sf.samtools.Cigar.<init>(Cigar.java:40) | |
| TRACE 301535: | |
| org.broad.igv.feature.genome.SequenceHelper.getSequence(SequenceHelper.java:134) | |
| org.broad.igv.feature.genome.GenomeImpl.getSequence(GenomeImpl.java:356) | |
| org.broad.igv.sam.BisulfiteCounts.incrementCounts(BisulfiteCounts.java:51) | |
| TRACE 301536: | |
| org.broad.igv.sam.BisulfiteCounts.incrementCounts(BisulfiteCounts.java:32) | |
| org.broad.igv.sam.BaseAlignmentCounts.incCounts(BaseAlignmentCounts.java:74) | |
| org.broad.igv.sam.CachingQueryReader$AlignmentTile.addRecord(CachingQueryReader.java:602) | |
| TRACE 301537: | |
| java.util.concurrent.atomic.AtomicLong.compareAndSet(AtomicLong.java:149) | |
| java.util.Random.next(Random.java:154) | |
| java.util.Random.nextDouble(Random.java:409) | |
| TRACE 301539: | |
| net.sf.samtools.SAMRecord.getDuplicateReadFlag(SAMRecord.java:771) | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:123) | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) | |
| TRACE 301541: | |
| org.broad.igv.sam.CachingQueryReader$AlignmentTile.access$400(CachingQueryReader.java:523) | |
| org.broad.igv.sam.CachingQueryReader$AlignmentTile$SamplingBucket.add(CachingQueryReader.java:727) | |
| org.broad.igv.sam.CachingQueryReader$AlignmentTile.addRecord(CachingQueryReader.java:618) | |
| TRACE 301542: | |
| org.broad.igv.sam.PEStats.update(PEStats.java:61) | |
| org.broad.igv.sam.CachingQueryReader.loadTiles(CachingQueryReader.java:350) | |
| org.broad.igv.sam.CachingQueryReader.getTiles(CachingQueryReader.java:218) | |
| TRACE 301543: | |
| org.broad.igv.sam.CachingQueryReader$AlignmentTile$SamplingBucket.add(CachingQueryReader.java:736) | |
| org.broad.igv.sam.CachingQueryReader$AlignmentTile.addRecord(CachingQueryReader.java:618) | |
| org.broad.igv.sam.CachingQueryReader.loadTiles(CachingQueryReader.java:327) | |
| TRACE 301549: | |
| net.sf.samtools.SAMRecord.getMappingQuality(SAMRecord.java:571) | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:120) | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) | |
| TRACE 301551: | |
| org.broad.igv.sam.CachingQueryReader$AlignmentTile.addRecord(CachingQueryReader.java:604) | |
| org.broad.igv.sam.CachingQueryReader.loadTiles(CachingQueryReader.java:327) | |
| org.broad.igv.sam.CachingQueryReader.getTiles(CachingQueryReader.java:218) | |
| TRACE 301552: | |
| net.sf.samtools.SAMRecord.getProperPairFlagUnchecked(SAMRecord.java:688) | |
| net.sf.samtools.SAMRecord.getProperPairFlag(SAMRecord.java:684) | |
| org.broad.igv.sam.SamAlignment.setMatePair(SamAlignment.java:169) | |
| TRACE 301553: | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:111) | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) | |
| TRACE 301555: | |
| org.broad.igv.sam.CachingQueryReader.loadTiles(CachingQueryReader.java:270) | |
| org.broad.igv.sam.CachingQueryReader.getTiles(CachingQueryReader.java:218) | |
| org.broad.igv.sam.CachingQueryReader.query(CachingQueryReader.java:140) | |
| TRACE 301558: | |
| org.broad.igv.sam.CachingQueryReader.loadTiles(CachingQueryReader.java:331) | |
| org.broad.igv.sam.CachingQueryReader.getTiles(CachingQueryReader.java:218) | |
| org.broad.igv.sam.CachingQueryReader.query(CachingQueryReader.java:140) | |
| TRACE 301570: | |
| javax.swing.JComponent.paintChildren(JComponent.java:789) | |
| javax.swing.JComponent.paint(JComponent.java:1038) | |
| javax.swing.JComponent.paintChildren(JComponent.java:866) | |
| TRACE 301572: | |
| java.util.HashMap.removeEntryForKey(HashMap.java:565) | |
| java.util.HashMap.remove(HashMap.java:555) | |
| org.broad.igv.util.ObjectCache.remove(ObjectCache.java:85) | |
| TRACE 301584: | |
| java.util.HashMap.put(HashMap.java:389) | |
| org.broad.igv.util.ObjectCache.put(ObjectCache.java:66) | |
| org.broad.igv.sam.CachingQueryReader.loadTiles(CachingQueryReader.java:300) | |
| TRACE 301585: | |
| java.util.LinkedHashMap.get(LinkedHashMap.java:297) | |
| org.broad.igv.util.ObjectCache.get(ObjectCache.java:72) | |
| org.broad.igv.sam.CachingQueryReader.loadTiles(CachingQueryReader.java:286) | |
| TRACE 301590: | |
| java.lang.Object.hashCode(Object.java:Unknown line) | |
| java.util.concurrent.ConcurrentHashMap.get(ConcurrentHashMap.java:796) | |
| sun.awt.image.SurfaceManager.getCacheData(SurfaceManager.java:114) | |
| TRACE 301594: | |
| org.apache.commons.math.util.FastMath.quadMult(FastMath.java:1130) | |
| org.apache.commons.math.util.FastMath.expint(FastMath.java:1207) | |
| org.apache.commons.math.util.FastMath.<clinit>(FastMath.java:218) | |
| TRACE 301595: | |
| org.apache.commons.math.util.FastMath.quadMult(FastMath.java:1130) | |
| org.apache.commons.math.util.FastMath.expint(FastMath.java:1203) | |
| org.apache.commons.math.util.FastMath.<clinit>(FastMath.java:218) | |
| TRACE 301596: | |
| org.apache.commons.math.util.FastMath.<clinit>(FastMath.java:231) | |
| org.apache.commons.math.stat.descriptive.rank.Percentile.evaluate(Percentile.java:272) | |
| org.apache.commons.math.stat.StatUtils.percentile(StatUtils.java:553) | |
| TRACE 301597: | |
| org.apache.commons.math.util.FastMath.slowLog(FastMath.java:1747) | |
| org.apache.commons.math.util.FastMath.<clinit>(FastMath.java:240) | |
| org.apache.commons.math.stat.descriptive.rank.Percentile.evaluate(Percentile.java:272) | |
| TRACE 301599: | |
| java.util.Arrays.mergeSort(Arrays.java:1278) | |
| java.util.Arrays.mergeSort(Arrays.java:1294) | |
| java.util.Arrays.mergeSort(Arrays.java:1295) | |
| TRACE 301600: | |
| java.util.Arrays.mergeSort(Arrays.java:1278) | |
| java.util.Arrays.mergeSort(Arrays.java:1295) | |
| java.util.Arrays.mergeSort(Arrays.java:1295) | |
| TRACE 301601: | |
| java.util.Arrays.mergeSort(Arrays.java:1278) | |
| java.util.Arrays.mergeSort(Arrays.java:1294) | |
| java.util.Arrays.mergeSort(Arrays.java:1294) | |
| TRACE 301602: | |
| java.util.ArrayList$ListItr.set(ArrayList.java:826) | |
| java.util.Collections.sort(Collections.java:180) | |
| org.broad.igv.sam.CachingQueryReader.query(CachingQueryReader.java:171) | |
| TRACE 301603: | |
| org.broad.igv.sam.CachingQueryReader$TiledIterator.advanceToNextRecord(CachingQueryReader.java:488) | |
| org.broad.igv.sam.CachingQueryReader$TiledIterator.next(CachingQueryReader.java:474) | |
| org.broad.igv.sam.CachingQueryReader$TiledIterator.next(CachingQueryReader.java:447) | |
| TRACE 301604: | |
| org.broad.igv.sam.AlignmentInterval$Row.addAlignment(AlignmentInterval.java:284) | |
| org.broad.igv.sam.AlignmentPacker.pack(AlignmentPacker.java:246) | |
| org.broad.igv.sam.AlignmentPacker.packAlignments(AlignmentPacker.java:75) | |
| TRACE 301608: | |
| sun.awt.X11GraphicsEnvironment.specificFontIDForName(X11GraphicsEnvironment.java:584) | |
| sun.awt.X11GraphicsEnvironment.registerFontDir(X11GraphicsEnvironment.java:857) | |
| sun.awt.X11GraphicsEnvironment.registerFontDirs(X11GraphicsEnvironment.java:761) | |
| TRACE 301610: | |
| sun.font.Type1Font.nextTokenType(Type1Font.java:584) | |
| sun.font.Type1Font.initNames(Type1Font.java:373) | |
| sun.font.Type1Font.verify(Type1Font.java:303) | |
| TRACE 301613: | |
| sun.misc.Unsafe.compareAndSwapInt(Unsafe.java:Unknown line) | |
| java.util.concurrent.atomic.AtomicInteger.compareAndSet(AtomicInteger.java:135) | |
| java.util.concurrent.atomic.AtomicInteger.decrementAndGet(AtomicInteger.java:220) | |
| TRACE 301624: | |
| sun.misc.Unsafe.compareAndSwapInt(Unsafe.java:Unknown line) | |
| java.util.concurrent.locks.AbstractQueuedSynchronizer.compareAndSetState(AbstractQueuedSynchronizer.java:570) | |
| java.util.concurrent.locks.ReentrantLock$NonfairSync.lock(ReentrantLock.java:211) | |
| TRACE 301625: | |
| java.awt.geom.Path2D$Float.<init>(Path2D.java:222) | |
| java.awt.geom.Path2D$Float.<init>(Path2D.java:207) | |
| sun.java2d.x11.X11Renderer.doPath(X11Renderer.java:306) | |
| TRACE 301632: | |
| java.awt.geom.Path2D$Float.<init>(Path2D.java:234) | |
| java.awt.geom.Path2D$Float.<init>(Path2D.java:207) | |
| sun.java2d.x11.X11Renderer.doPath(X11Renderer.java:306) | |
| TRACE 301636: | |
| org.broad.igv.sam.CoverageTrack$IntervalRenderer.paint(CoverageTrack.java:306) | |
| org.broad.igv.sam.CoverageTrack$IntervalRenderer.access$000(CoverageTrack.java:277) | |
| org.broad.igv.sam.CoverageTrack.render(CoverageTrack.java:170) | |
| TRACE 301640: | |
| sun.java2d.pisces.Dasher.<init>(Dasher.java:94) | |
| sun.java2d.pisces.PiscesRenderingEngine.strokeTo(PiscesRenderingEngine.java:349) | |
| sun.java2d.pisces.PiscesRenderingEngine.strokeTo(PiscesRenderingEngine.java:164) | |
| TRACE 301641: | |
| java.lang.StrictMath.pow(StrictMath.java:Unknown line) | |
| java.lang.Math.pow(Math.java:626) | |
| org.broad.igv.ui.panel.RulerPanel.findSpacing(RulerPanel.java:331) | |
| TRACE 301648: | |
| java.lang.System.nanoTime(System.java:Unknown line) | |
| javax.swing.TimerQueue.now(TimerQueue.java:226) | |
| javax.swing.TimerQueue.access$000(TimerQueue.java:47) | |
| TRACE 301650: | |
| java.lang.System.arraycopy(System.java:Unknown line) | |
| java.io.ByteArrayOutputStream.write(ByteArrayOutputStream.java:113) | |
| org.broad.igv.feature.genome.FastaIndexedSequence.readSequence(FastaIndexedSequence.java:127) | |
| TRACE 301651: | |
| org.broad.igv.sam.DenseAlignmentCounts.<init>(DenseAlignmentCounts.java:77) | |
| org.broad.igv.sam.CachingQueryReader$AlignmentTile.<init>(CachingQueryReader.java:559) | |
| org.broad.igv.sam.CachingQueryReader.getTiles(CachingQueryReader.java:197) | |
| TRACE 301652: | |
| net.sf.samtools.util.BinaryCodec.readByteBuffer(BinaryCodec.java:480) | |
| net.sf.samtools.util.BinaryCodec.readInt(BinaryCodec.java:491) | |
| net.sf.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:189) | |
| TRACE 301653: | |
| org.broad.igv.sam.SamAlignment.createAlignmentBlocks(SamAlignment.java:519) | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:150) | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) | |
| TRACE 301655: | |
| java.util.HashMap.put(HashMap.java:389) | |
| org.broad.igv.util.ObjectCache.put(ObjectCache.java:66) | |
| org.broad.igv.sam.CachingQueryReader.loadTiles(CachingQueryReader.java:288) | |
| TRACE 301657: | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:117) | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33) | |
| TRACE 301658: | |
| java.util.concurrent.ConcurrentHashMap$Segment.getFirst(ConcurrentHashMap.java:341) | |
| java.util.concurrent.ConcurrentHashMap$Segment.get(ConcurrentHashMap.java:364) | |
| java.util.concurrent.ConcurrentHashMap.get(ConcurrentHashMap.java:797) | |
| TRACE 301661: | |
| sun.java2d.SunGraphics2D.clone(SunGraphics2D.java:266) | |
| sun.java2d.SunGraphics2D.create(SunGraphics2D.java:299) | |
| javax.swing.JComponent.paintComponent(JComponent.java:763) | |
| TRACE 301663: | |
| net.sf.samtools.SAMReadGroupRecord.getSample(SAMReadGroupRecord.java:66) | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:142) | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) | |
| TRACE 301664: | |
| org.broad.igv.sam.SamAlignment.setMatePair(SamAlignment.java:168) | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:131) | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) | |
| TRACE 301666: | |
| java.util.HashMap.containsKey(HashMap.java:352) | |
| org.broad.igv.feature.genome.GenomeImpl.getChromosomeAlias(GenomeImpl.java:110) | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:112) | |
| TRACE 301667: | |
| net.sf.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:192) | |
| net.sf.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:523) | |
| net.sf.samtools.BAMFileReader$BAMFileIndexIterator.getNextRecord(BAMFileReader.java:630) | |
| TRACE 301668: | |
| org.broad.igv.sam.AlignmentTrack.getBisulfiteContextPreContext(AlignmentTrack.java:744) | |
| org.broad.igv.sam.BisulfiteCounts.contextIsMatching(BisulfiteCounts.java:143) | |
| org.broad.igv.sam.BisulfiteCounts.incrementCounts(BisulfiteCounts.java:83) | |
| TRACE 301669: | |
| java.util.HashMap.get(HashMap.java:320) | |
| org.broad.igv.feature.genome.GenomeImpl.getChromosomeAlias(GenomeImpl.java:111) | |
| org.broad.igv.sam.SamAlignment.setMatePair(SamAlignment.java:168) | |
| TRACE 301672: | |
| java.util.LinkedHashMap.get(LinkedHashMap.java:297) | |
| org.broad.igv.util.ObjectCache.get(ObjectCache.java:72) | |
| org.broad.igv.feature.genome.SequenceHelper.getSequenceTile(SequenceHelper.java:188) | |
| TRACE 301673: | |
| net.sf.samtools.BinaryCigarCodec.decode(BinaryCigarCodec.java:70) | |
| net.sf.samtools.BAMRecord.getCigar(BAMRecord.java:243) | |
| net.sf.samtools.SAMRecord.getAlignmentEnd(SAMRecord.java:456) | |
| TRACE 301676: | |
| net.sf.samtools.SAMReadGroupRecord.getFlowOrder(SAMReadGroupRecord.java:84) | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:144) | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50) | |
| TRACE 301678: | |
| javax.swing.JComponent.rectangleIsObscured(JComponent.java:4354) | |
| javax.swing.JComponent.paint(JComponent.java:1027) | |
| javax.swing.JComponent.paintChildren(JComponent.java:866) | |
| TRACE 301679: | |
| net.sf.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:67) | |
| net.sf.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:379) | |
| net.sf.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:361) | |
| TRACE 301680: | |
| java.util.HashMap.get(HashMap.java:320) | |
| org.broad.igv.feature.genome.GenomeImpl.getChromosomeAlias(GenomeImpl.java:111) | |
| org.broad.igv.sam.BisulfiteCounts.incrementCounts(BisulfiteCounts.java:34) | |
| TRACE 301681: | |
| sun.java2d.SunGraphics2D.transformShape(SunGraphics2D.java:1900) | |
| sun.java2d.SunGraphics2D.transformShape(SunGraphics2D.java:1875) | |
| sun.java2d.SunGraphics2D.setClip(SunGraphics2D.java:1961) | |
| TRACE 301682: | |
| javax.swing.JComponent.fetchRectangle(JComponent.java:438) | |
| javax.swing.JComponent.getObscuredState(JComponent.java:5165) | |
| javax.swing.JComponent.paintChildren(JComponent.java:839) | |
| TRACE 301683: | |
| javax.swing.JComponent.rectangleIsObscured(JComponent.java:4354) | |
| javax.swing.JComponent.paint(JComponent.java:1027) | |
| javax.swing.JComponent.paintChildren(JComponent.java:866) | |
| TRACE 301684: | |
| java.util.Arrays.mergeSort(Arrays.java:1306) | |
| java.util.Arrays.mergeSort(Arrays.java:1295) | |
| java.util.Arrays.sort(Arrays.java:1223) | |
| TRACE 301685: | |
| org.broad.igv.sam.AlignmentPacker.pack(AlignmentPacker.java:245) | |
| org.broad.igv.sam.AlignmentPacker.packAlignments(AlignmentPacker.java:75) | |
| org.broad.igv.sam.AlignmentDataManager$2.run(AlignmentDataManager.java:324) | |
| TRACE 301686: | |
| java.util.HashMap$ValueIterator.next(HashMap.java:839) | |
| org.broad.igv.track.RenderContextImpl.dispose(RenderContextImpl.java:130) | |
| org.broad.igv.ui.panel.DataPanel.paintComponent(DataPanel.java:168) | |
| TRACE 301688: | |
| javax.swing.border.CompoundBorder.getBorderInsets(CompoundBorder.java:133) | |
| javax.swing.border.CompoundBorder.getBorderInsets(CompoundBorder.java:157) | |
| javax.swing.JComponent.getInsets(JComponent.java:1796) | |
| TRACE 301690: | |
| org.broad.igv.PreferenceManager.getAsBoolean(PreferenceManager.java:256) | |
| org.broad.igv.sam.SamAlignment.createAlignmentBlocks(SamAlignment.java:432) | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:150) | |
| TRACE 301694: | |
| java.lang.Integer.getChars(Integer.java:370) | |
| java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:615) | |
| java.lang.StringBuilder.append(StringBuilder.java:229) | |
| TRACE 301695: | |
| sun.java2d.x11.X11PMBlitLoops.nativeBlit(X11PMBlitLoops.java:Unknown line) | |
| sun.java2d.x11.X11PMBlitLoops.Blit(X11PMBlitLoops.java:143) | |
| sun.java2d.pipe.DrawImage.blitSurfaceData(DrawImage.java:956) | |
| TRACE 301696: | |
| org.broad.igv.sam.CachingQueryReader$AlignmentTile.emptyBucket(CachingQueryReader.java:630) | |
| org.broad.igv.sam.CachingQueryReader$AlignmentTile.addRecord(CachingQueryReader.java:608) | |
| org.broad.igv.sam.CachingQueryReader.loadTiles(CachingQueryReader.java:327) | |
| TRACE 301698: | |
| sun.java2d.SunGraphics2D.constrain(SunGraphics2D.java:329) | |
| java.awt.Component.getGraphics(Component.java:2799) | |
| javax.swing.JComponent.getGraphics(JComponent.java:1932) | |
| TRACE 301700: | |
| net.sf.samtools.BAMFileReader$BAMQueryFilteringIterator.advance(BAMFileReader.java:737) | |
| net.sf.samtools.BAMFileReader$BAMQueryFilteringIterator.next(BAMFileReader.java:685) | |
| net.sf.samtools.BAMFileReader$BAMQueryFilteringIterator.next(BAMFileReader.java:638) | |
| TRACE 301701: | |
| sun.swing.SwingUtilities2.stringWidth(SwingUtilities2.java:351) | |
| javax.swing.SwingUtilities.layoutCompoundLabelImpl(SwingUtilities.java:1002) | |
| javax.swing.SwingUtilities.layoutCompoundLabel(SwingUtilities.java:887) | |
| TRACE 301702: | |
| net.sf.samtools.SAMRecord.getAlignmentEnd(SAMRecord.java:456) | |
| net.sf.samtools.BAMFileReader$BAMQueryFilteringIterator.advance(BAMFileReader.java:737) | |
| net.sf.samtools.BAMFileReader$BAMQueryFilteringIterator.next(BAMFileReader.java:685) | |
| TRACE 301703: | |
| java.util.HashMap.containsKey(HashMap.java:352) | |
| org.broad.igv.feature.genome.GenomeImpl.getChromosomeAlias(GenomeImpl.java:110) | |
| org.broad.igv.sam.SamAlignment.setMatePair(SamAlignment.java:168) | |
| TRACE 301704: | |
| java.awt.Component.repaint(Component.java:3074) | |
| javax.swing.JLabel.setText(JLabel.java:343) | |
| org.broad.igv.ui.util.ApplicationStatusBar$1.run(ApplicationStatusBar.java:93) | |
| TRACE 301707: | |
| java.util.LinkedHashMap.get(LinkedHashMap.java:297) | |
| org.broad.igv.feature.genome.GenomeImpl.getChromosome(GenomeImpl.java:240) | |
| org.broad.igv.feature.genome.GenomeImpl.getSequence(GenomeImpl.java:348) | |
| TRACE 301708: | |
| java.awt.geom.AffineTransform.translate(AffineTransform.java:1247) | |
| sun.java2d.SunGraphics2D.translate(SunGraphics2D.java:1519) | |
| javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1452) | |
| TRACE 301709: | |
| java.util.zip.Inflater.reset(Inflater.java:Unknown line) | |
| java.util.zip.Inflater.reset(Inflater.java:345) | |
| net.sf.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:92) | |
| TRACE 301710: | |
| org.broad.igv.feature.genome.GenomeImpl.getChromosome(GenomeImpl.java:240) | |
| org.broad.igv.feature.genome.GenomeImpl.getSequence(GenomeImpl.java:348) | |
| org.broad.igv.sam.BisulfiteCounts.incrementCounts(BisulfiteCounts.java:51) | |
| TRACE 301711: | |
| java.util.Arrays.mergeSort(Arrays.java:1306) | |
| java.util.Arrays.mergeSort(Arrays.java:1295) | |
| java.util.Arrays.mergeSort(Arrays.java:1295) | |
| TRACE 301715: | |
| sun.java2d.pipe.ShapeSpanIterator.lineTo(ShapeSpanIterator.java:Unknown line) | |
| sun.java2d.pisces.Stroker.emitLineTo(Stroker.java:455) | |
| sun.java2d.pisces.Stroker.lineTo(Stroker.java:370) | |
| CPU SAMPLES BEGIN (total = 3814) Fri Jul 19 08:47:42 2013 | |
| rank self accum count trace method | |
| 1 36.42% 36.42% 1389 300769 sun.awt.X11.XToolkit.waitForEvents | |
| 2 35.79% 72.21% 1365 301479 java.net.PlainSocketImpl.socketAccept | |
| 3 3.75% 75.96% 143 301560 org.broad.igv.feature.ChromosomeImpl.getLength | |
| 4 1.99% 77.95% 76 301569 java.util.zip.Inflater.inflateBytes | |
| 5 1.97% 79.92% 75 301561 org.broad.igv.feature.ChromosomeImpl.getLength | |
| 6 1.26% 81.17% 48 301557 org.broad.igv.sam.DenseAlignmentCounts.incBlockCounts | |
| 7 1.10% 82.28% 42 301575 net.sf.samtools.BAMRecord.decodeReadBases | |
| 8 1.00% 83.27% 38 301563 net.sf.samtools.util.BlockCompressedInputStream.read | |
| 9 0.92% 84.19% 35 301562 net.sf.samtools.BinaryTagCodec.readTags | |
| 10 0.87% 85.06% 33 301573 java.lang.Integer.hashCode | |
| 11 0.60% 85.66% 23 301510 sun.java2d.loops.DrawGlyphListAA.DrawGlyphListAA | |
| 12 0.50% 86.16% 19 301656 org.broad.igv.sam.BisulfiteCounts.incrementCounts | |
| 13 0.42% 86.58% 16 301577 org.broad.igv.sam.SamAlignment.createAlignmentBlocks | |
| 14 0.39% 86.97% 15 301567 java.util.HashMap.getEntry | |
| 15 0.37% 87.34% 14 301578 net.sf.samtools.util.StringUtil.bytesToString | |
| 16 0.37% 87.70% 14 301586 java.lang.Integer.parseInt | |
| 17 0.37% 88.07% 14 301587 sun.java2d.x11.X11SurfaceData.XSetForeground | |
| 18 0.34% 88.41% 13 301564 net.sf.samtools.BinaryCigarCodec.decode | |
| 19 0.34% 88.75% 13 301566 java.util.Hashtable.get | |
| 20 0.31% 89.07% 12 301559 java.nio.ByteBuffer.get | |
| 21 0.31% 89.38% 12 301639 sun.java2d.x11.X11Renderer.XDoPath | |
| 22 0.26% 89.64% 10 301634 sun.java2d.x11.X11Renderer.XFillRect | |
| 23 0.24% 89.88% 9 301571 net.sf.samtools.util.BlockCompressedInputStream.inflateBlock | |
| 24 0.21% 90.09% 8 301593 org.broad.igv.sam.SamAlignment.createAlignmentBlocks | |
| 25 0.21% 90.30% 8 301638 sun.java2d.x11.X11Renderer.XDoPath | |
| 26 0.18% 90.48% 7 301418 java.net.SocketInputStream.socketRead0 | |
| 27 0.18% 90.67% 7 301534 net.sf.samtools.BAMRecordCodec.decode | |
| 28 0.18% 90.85% 7 301576 java.lang.StringBuffer.append | |
| 29 0.16% 91.01% 6 301554 org.broad.igv.sam.CachingQueryReader.loadTiles | |
| 30 0.16% 91.16% 6 301556 java.io.RandomAccessFile.readBytes | |
| 31 0.16% 91.32% 6 301565 java.util.ArrayList.iterator | |
| 32 0.16% 91.48% 6 301568 org.broad.igv.sam.reader.WrappedIterator.next | |
| 33 0.16% 91.64% 6 301580 net.sf.samtools.BAMFileReader$BAMFileIterator.next | |
| 34 0.16% 91.79% 6 301665 org.broad.igv.sam.CachingQueryReader$AlignmentTile.addRecord | |
| 35 0.13% 91.92% 5 300275 java.lang.ClassLoader.defineClass1 | |
| 36 0.13% 92.06% 5 300772 java.io.FileInputStream.readBytes | |
| 37 0.13% 92.19% 5 300773 java.lang.UNIXProcess.waitForProcessExit | |
| 38 0.13% 92.32% 5 301662 java.util.ArrayList.iterator | |
| 39 0.10% 92.42% 4 300022 java.lang.String.intern | |
| 40 0.10% 92.53% 4 301328 sun.awt.X11.XlibWrapper.XSync | |
| 41 0.10% 92.63% 4 301550 net.sf.samtools.BAMRecord.decodeBaseQualities | |
| 42 0.10% 92.74% 4 301631 sun.java2d.pipe.ShapeSpanIterator.setNormalize | |
| 43 0.10% 92.84% 4 301642 sun.java2d.x11.X11Renderer.XDrawLine | |
| 44 0.10% 92.95% 4 301654 net.sf.samtools.SAMBinaryTagAndValue.insert | |
| 45 0.10% 93.05% 4 301689 java.security.AccessController.getStackAccessControlContext | |
| 46 0.10% 93.16% 4 301699 java.lang.StringBuilder.append | |
| 47 0.08% 93.24% 3 300020 java.lang.StringCoding$StringDecoder.decode | |
| 48 0.08% 93.31% 3 300100 java.util.zip.Inflater.inflateBytes | |
| 49 0.08% 93.39% 3 301533 java.lang.System.arraycopy | |
| 50 0.08% 93.47% 3 301544 org.broad.igv.sam.CachingQueryReader$AlignmentTile.addRecord | |
| 51 0.08% 93.55% 3 301545 org.broad.igv.sam.SamAlignment.setPairOrientation | |
| 52 0.08% 93.63% 3 301574 org.broad.igv.sam.CachingQueryReader.loadTiles | |
| 53 0.08% 93.71% 3 301583 org.broad.igv.sam.SamAlignment.<init> | |
| 54 0.08% 93.79% 3 301633 java.lang.StrictMath.ceil | |
| 55 0.08% 93.86% 3 301635 org.broad.igv.sam.AlignmentRenderer.drawAlignment | |
| 56 0.08% 93.94% 3 301649 sun.misc.Unsafe.compareAndSwapInt | |
| 57 0.08% 94.02% 3 301659 java.lang.StringBuilder.append | |
| 58 0.08% 94.10% 3 301660 org.broad.igv.sam.CachingQueryReader.loadTiles | |
| 59 0.08% 94.18% 3 301670 java.util.HashMap.get | |
| 60 0.08% 94.26% 3 301691 java.util.Collections$UnmodifiableCollection$1.<init> | |
| 61 0.08% 94.34% 3 301693 net.sf.samtools.SAMReadGroupRecord.getPlatform | |
| 62 0.08% 94.42% 3 301705 net.sf.samtools.util.StringUtil.bytesToString | |
| 63 0.08% 94.49% 3 301706 net.sf.samtools.util.StringUtil.bytesToString | |
| 64 0.05% 94.55% 2 300257 sun.security.provider.DigestBase.engineUpdate | |
| 65 0.05% 94.60% 2 300260 java.util.HashMap$HashIterator.nextEntry | |
| 66 0.05% 94.65% 2 301352 sun.awt.X11.XlibWrapper.XQueryTree | |
| 67 0.05% 94.70% 2 301419 sun.awt.X11.XlibWrapper.XGetWindowAttributes | |
| 68 0.05% 94.76% 2 301513 java.security.AccessController.doPrivileged | |
| 69 0.05% 94.81% 2 301529 org.broad.igv.sam.SamAlignment.createAlignmentBlocks | |
| 70 0.05% 94.86% 2 301540 net.sf.samtools.BAMRecord.decodeBaseQualities | |
| 71 0.05% 94.91% 2 301579 net.sf.samtools.SAMBinaryTagAndValue.find | |
| 72 0.05% 94.97% 2 301581 net.sf.samtools.SAMRecord.getCigarString | |
| 73 0.05% 95.02% 2 301582 org.broad.igv.sam.CachingQueryReader$AlignmentTile.addRecord | |
| 74 0.05% 95.07% 2 301588 net.sf.samtools.SAMReadGroupRecord.getKeySequence | |
| 75 0.05% 95.12% 2 301589 java.lang.Object.clone | |
| 76 0.05% 95.18% 2 301591 java.util.Hashtable.get | |
| 77 0.05% 95.23% 2 301592 org.broad.igv.sam.BaseAlignmentCounts.incCounts | |
| 78 0.05% 95.28% 2 301598 java.util.Arrays.mergeSort | |
| 79 0.05% 95.33% 2 301637 sun.java2d.pisces.Stroker.<init> | |
| 80 0.05% 95.39% 2 301647 sun.java2d.loops.MaskBlit.MaskBlit | |
| 81 0.05% 95.44% 2 301671 net.sf.samtools.BAMRecordCodec.decode | |
| 82 0.05% 95.49% 2 301674 net.sf.samtools.Cigar.isEmpty | |
| 83 0.05% 95.54% 2 301675 sun.font.X11TextRenderer.doDrawGlyphList | |
| 84 0.05% 95.60% 2 301677 java.util.HashMap.get | |
| 85 0.05% 95.65% 2 301687 java.security.AccessController.doPrivileged | |
| 86 0.05% 95.70% 2 301692 java.awt.Component.getGraphicsConfiguration | |
| 87 0.05% 95.75% 2 301697 org.broad.igv.feature.ChromosomeImpl.getLength | |
| 88 0.03% 95.78% 1 300001 java.lang.ClassLoader.findBootstrapClass | |
| 89 0.03% 95.80% 1 300016 java.util.jar.Manifest.read | |
| 90 0.03% 95.83% 1 300017 java.lang.String.<init> | |
| 91 0.03% 95.86% 1 300018 java.util.HashMap.<init> | |
| 92 0.03% 95.88% 1 300019 java.util.jar.Attributes.read | |
| 93 0.03% 95.91% 1 300033 sun.misc.URLClassPath$JarLoader.checkResource | |
| 94 0.03% 95.94% 1 300105 java.util.Arrays.copyOfRange | |
| 95 0.03% 95.96% 1 300106 java.lang.AbstractStringBuilder.<init> | |
| 96 0.03% 95.99% 1 300151 sun.security.x509.RDN.<init> | |
| 97 0.03% 96.01% 1 300232 java.io.BufferedInputStream.read | |
| 98 0.03% 96.04% 1 300250 sun.security.provider.SHA.implCompress | |
| 99 0.03% 96.07% 1 300251 sun.misc.Unsafe.getInt | |
| 100 0.03% 96.09% 1 300276 org.broad.igv.ui.Main.<clinit> | |
| 101 0.03% 96.12% 1 300297 java.util.HashMap.createEntry | |
| 102 0.03% 96.15% 1 300298 sun.security.util.ManifestDigester.<init> | |
| 103 0.03% 96.17% 1 300299 java.lang.Throwable.fillInStackTrace | |
| 104 0.03% 96.20% 1 300355 sun.util.resources.LocaleData$1.run | |
| 105 0.03% 96.22% 1 300420 com.sun.org.apache.xerces.internal.parsers.XML11Configuration.<init> | |
| 106 0.03% 96.25% 1 300482 com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.doctypeDecl | |
| 107 0.03% 96.28% 1 300530 javax.swing.filechooser.FileSystemView.getFileSystemView | |
| 108 0.03% 96.30% 1 300572 sun.awt.X11GraphicsEnvironment.initDisplay | |
| 109 0.03% 96.33% 1 300592 java.lang.Class.forName0 | |
| 110 0.03% 96.36% 1 300622 java.lang.String.equals | |
| 111 0.03% 96.38% 1 300667 sun.java2d.NullSurfaceData.<init> | |
| 112 0.03% 96.41% 1 300740 sun.awt.X11.XToolkit.keysymToPrimaryKeycode | |
| 113 0.03% 96.43% 1 300770 java.lang.UNIXProcess$1$1.run | |
| 114 0.03% 96.46% 1 300794 java.awt.KeyboardFocusManager.<init> | |
| 115 0.03% 96.49% 1 300831 javax.swing.LookAndFeel.installProperty | |
| 116 0.03% 96.51% 1 300853 java.lang.String.toUpperCase | |
| 117 0.03% 96.54% 1 300858 java.util.HashMap$HashIterator.<init> | |
| 118 0.03% 96.57% 1 300924 java.io.RandomAccessFile.seek | |
| 119 0.03% 96.59% 1 300935 java.lang.StrictMath.floor | |
| 120 0.03% 96.62% 1 300948 com.sun.imageio.plugins.gif.GIFImageReader.initializeStringTable | |
| 121 0.03% 96.64% 1 300949 java.lang.String.concat | |
| 122 0.03% 96.67% 1 300969 org.broad.igv.session.Session.<init> | |
| 123 0.03% 96.70% 1 300991 java.util.Vector.removeElementAt | |
| 124 0.03% 96.72% 1 301004 sun.awt.X11.XlibWrapper.XQueryBestCursor | |
| 125 0.03% 96.75% 1 301008 javax.swing.JComboBox.installAncestorListener | |
| 126 0.03% 96.78% 1 301055 sun.awt.X11.XlibWrapper.InternAtom | |
| 127 0.03% 96.80% 1 301095 javax.swing.plaf.basic.BasicComboBoxEditor.createEditorComponent | |
| 128 0.03% 96.83% 1 301184 javax.swing.plaf.metal.MetalComboBoxUI.createArrowButton | |
| 129 0.03% 96.85% 1 301189 java.util.zip.ZipFile.getEntry | |
| 130 0.03% 96.88% 1 301190 javax.swing.ArrayTable.put | |
| 131 0.03% 96.91% 1 301196 sun.security.util.ManifestEntryVerifier.setEntry | |
| 132 0.03% 96.93% 1 301197 java.util.Collections.synchronizedList | |
| 133 0.03% 96.96% 1 301198 java.awt.Component.repaint | |
| 134 0.03% 96.98% 1 301204 org.broad.igv.ui.util.MenuAndToolbarUtils.createMenuItem | |
| 135 0.03% 97.01% 1 301219 javax.swing.DefaultButtonModel.addChangeListener | |
| 136 0.03% 97.04% 1 301224 javax.swing.UIManager.maybeInitialize | |
| 137 0.03% 97.06% 1 301244 java.util.Arrays.binarySearch0 | |
| 138 0.03% 97.09% 1 301245 sun.awt.X11.XEvent.get_xany | |
| 139 0.03% 97.12% 1 301284 sun.awt.X11.XDragAndDropProtocols.<clinit> | |
| 140 0.03% 97.14% 1 301308 sun.nio.cs.UTF_16.newDecoder | |
| 141 0.03% 97.17% 1 301330 java.lang.String.endsWith | |
| 142 0.03% 97.19% 1 301331 java.awt.Container.minimumSize | |
| 143 0.03% 97.22% 1 301406 java.net.Inet6AddressImpl.lookupAllHostAddr | |
| 144 0.03% 97.25% 1 301432 sun.awt.X11.XlibWrapper.XEventsQueued | |
| 145 0.03% 97.27% 1 301433 java.awt.Container.paint | |
| 146 0.03% 97.30% 1 301447 sun.awt.X11.XInputMethod.openXIMNative | |
| 147 0.03% 97.33% 1 301448 sun.awt.im.InputContext.focusGained | |
| 148 0.03% 97.35% 1 301461 java.awt.Container.addImpl | |
| 149 0.03% 97.38% 1 301462 java.util.ArrayList.add | |
| 150 0.03% 97.40% 1 301470 org.broad.igv.ui.panel.ReferenceFrame.setChromosomeName | |
| 151 0.03% 97.43% 1 301471 java.lang.Thread.currentThread | |
| 152 0.03% 97.46% 1 301478 sun.swing.CachedPainter.getCache | |
| 153 0.03% 97.48% 1 301492 sun.awt.X11.XlibWrapper.XSync | |
| 154 0.03% 97.51% 1 301504 javax.swing.plaf.metal.MetalComboBoxIcon.paintIcon | |
| 155 0.03% 97.54% 1 301505 java.awt.Component.getParent | |
| 156 0.03% 97.56% 1 301506 java.lang.String.concat | |
| 157 0.03% 97.59% 1 301507 sun.misc.Unsafe.getFloat | |
| 158 0.03% 97.61% 1 301508 sun.java2d.loops.MaskBlit.MaskBlit | |
| 159 0.03% 97.64% 1 301509 java.security.AccessController.getStackAccessControlContext | |
| 160 0.03% 97.67% 1 301511 sun.misc.Unsafe.unpark | |
| 161 0.03% 97.69% 1 301512 java.awt.EventQueue.getNextEvent | |
| 162 0.03% 97.72% 1 301522 java.security.MessageDigest$Delegate.engineUpdate | |
| 163 0.03% 97.75% 1 301526 java.lang.Object.hashCode | |
| 164 0.03% 97.77% 1 301527 java.util.HashMap.getEntry | |
| 165 0.03% 97.80% 1 301528 java.lang.System.arraycopy | |
| 166 0.03% 97.82% 1 301530 org.broad.igv.sam.SamAlignment.createAlignmentBlocks | |
| 167 0.03% 97.85% 1 301531 java.nio.Buffer.flip | |
| 168 0.03% 97.88% 1 301532 java.util.ArrayList.<init> | |
| 169 0.03% 97.90% 1 301535 org.broad.igv.feature.genome.SequenceHelper.getSequence | |
| 170 0.03% 97.93% 1 301536 org.broad.igv.sam.BisulfiteCounts.incrementCounts | |
| 171 0.03% 97.95% 1 301537 java.util.concurrent.atomic.AtomicLong.compareAndSet | |
| 172 0.03% 97.98% 1 301539 net.sf.samtools.SAMRecord.getDuplicateReadFlag | |
| 173 0.03% 98.01% 1 301541 org.broad.igv.sam.CachingQueryReader$AlignmentTile.access$400 | |
| 174 0.03% 98.03% 1 301542 org.broad.igv.sam.PEStats.update | |
| 175 0.03% 98.06% 1 301543 org.broad.igv.sam.CachingQueryReader$AlignmentTile$SamplingBucket.add | |
| 176 0.03% 98.09% 1 301549 net.sf.samtools.SAMRecord.getMappingQuality | |
| 177 0.03% 98.11% 1 301551 org.broad.igv.sam.CachingQueryReader$AlignmentTile.addRecord | |
| 178 0.03% 98.14% 1 301552 net.sf.samtools.SAMRecord.getProperPairFlagUnchecked | |
| 179 0.03% 98.16% 1 301553 org.broad.igv.sam.SamAlignment.<init> | |
| 180 0.03% 98.19% 1 301555 org.broad.igv.sam.CachingQueryReader.loadTiles | |
| 181 0.03% 98.22% 1 301558 org.broad.igv.sam.CachingQueryReader.loadTiles | |
| 182 0.03% 98.24% 1 301570 javax.swing.JComponent.paintChildren | |
| 183 0.03% 98.27% 1 301572 java.util.HashMap.removeEntryForKey | |
| 184 0.03% 98.30% 1 301584 java.util.HashMap.put | |
| 185 0.03% 98.32% 1 301585 java.util.LinkedHashMap.get | |
| 186 0.03% 98.35% 1 301590 java.lang.Object.hashCode | |
| 187 0.03% 98.37% 1 301594 org.apache.commons.math.util.FastMath.quadMult | |
| 188 0.03% 98.40% 1 301595 org.apache.commons.math.util.FastMath.quadMult | |
| 189 0.03% 98.43% 1 301596 org.apache.commons.math.util.FastMath.<clinit> | |
| 190 0.03% 98.45% 1 301597 org.apache.commons.math.util.FastMath.slowLog | |
| 191 0.03% 98.48% 1 301599 java.util.Arrays.mergeSort | |
| 192 0.03% 98.51% 1 301600 java.util.Arrays.mergeSort | |
| 193 0.03% 98.53% 1 301601 java.util.Arrays.mergeSort | |
| 194 0.03% 98.56% 1 301602 java.util.ArrayList$ListItr.set | |
| 195 0.03% 98.58% 1 301603 org.broad.igv.sam.CachingQueryReader$TiledIterator.advanceToNextRecord | |
| 196 0.03% 98.61% 1 301604 org.broad.igv.sam.AlignmentInterval$Row.addAlignment | |
| 197 0.03% 98.64% 1 301608 sun.awt.X11GraphicsEnvironment.specificFontIDForName | |
| 198 0.03% 98.66% 1 301610 sun.font.Type1Font.nextTokenType | |
| 199 0.03% 98.69% 1 301613 sun.misc.Unsafe.compareAndSwapInt | |
| 200 0.03% 98.72% 1 301624 sun.misc.Unsafe.compareAndSwapInt | |
| 201 0.03% 98.74% 1 301625 java.awt.geom.Path2D$Float.<init> | |
| 202 0.03% 98.77% 1 301632 java.awt.geom.Path2D$Float.<init> | |
| 203 0.03% 98.79% 1 301636 org.broad.igv.sam.CoverageTrack$IntervalRenderer.paint | |
| 204 0.03% 98.82% 1 301640 sun.java2d.pisces.Dasher.<init> | |
| 205 0.03% 98.85% 1 301641 java.lang.StrictMath.pow | |
| 206 0.03% 98.87% 1 301648 java.lang.System.nanoTime | |
| 207 0.03% 98.90% 1 301650 java.lang.System.arraycopy | |
| 208 0.03% 98.93% 1 301651 org.broad.igv.sam.DenseAlignmentCounts.<init> | |
| 209 0.03% 98.95% 1 301652 net.sf.samtools.util.BinaryCodec.readByteBuffer | |
| 210 0.03% 98.98% 1 301653 org.broad.igv.sam.SamAlignment.createAlignmentBlocks | |
| 211 0.03% 99.00% 1 301655 java.util.HashMap.put | |
| 212 0.03% 99.03% 1 301657 org.broad.igv.sam.SamAlignment.<init> | |
| 213 0.03% 99.06% 1 301658 java.util.concurrent.ConcurrentHashMap$Segment.getFirst | |
| 214 0.03% 99.08% 1 301661 sun.java2d.SunGraphics2D.clone | |
| 215 0.03% 99.11% 1 301663 net.sf.samtools.SAMReadGroupRecord.getSample | |
| 216 0.03% 99.13% 1 301664 org.broad.igv.sam.SamAlignment.setMatePair | |
| 217 0.03% 99.16% 1 301666 java.util.HashMap.containsKey | |
| 218 0.03% 99.19% 1 301667 net.sf.samtools.BAMRecordCodec.decode | |
| 219 0.03% 99.21% 1 301668 org.broad.igv.sam.AlignmentTrack.getBisulfiteContextPreContext | |
| 220 0.03% 99.24% 1 301669 java.util.HashMap.get | |
| 221 0.03% 99.27% 1 301672 java.util.LinkedHashMap.get | |
| 222 0.03% 99.29% 1 301673 net.sf.samtools.BinaryCigarCodec.decode | |
| 223 0.03% 99.32% 1 301676 net.sf.samtools.SAMReadGroupRecord.getFlowOrder | |
| 224 0.03% 99.34% 1 301678 javax.swing.JComponent.rectangleIsObscured | |
| 225 0.03% 99.37% 1 301679 net.sf.samtools.util.BlockGunzipper.unzipBlock | |
| 226 0.03% 99.40% 1 301680 java.util.HashMap.get | |
| 227 0.03% 99.42% 1 301681 sun.java2d.SunGraphics2D.transformShape | |
| 228 0.03% 99.45% 1 301682 javax.swing.JComponent.fetchRectangle | |
| 229 0.03% 99.48% 1 301683 javax.swing.JComponent.rectangleIsObscured | |
| 230 0.03% 99.50% 1 301684 java.util.Arrays.mergeSort | |
| 231 0.03% 99.53% 1 301685 org.broad.igv.sam.AlignmentPacker.pack | |
| 232 0.03% 99.55% 1 301686 java.util.HashMap$ValueIterator.next | |
| 233 0.03% 99.58% 1 301688 javax.swing.border.CompoundBorder.getBorderInsets | |
| 234 0.03% 99.61% 1 301690 org.broad.igv.PreferenceManager.getAsBoolean | |
| 235 0.03% 99.63% 1 301694 java.lang.Integer.getChars | |
| 236 0.03% 99.66% 1 301695 sun.java2d.x11.X11PMBlitLoops.nativeBlit | |
| 237 0.03% 99.69% 1 301696 org.broad.igv.sam.CachingQueryReader$AlignmentTile.emptyBucket | |
| 238 0.03% 99.71% 1 301698 sun.java2d.SunGraphics2D.constrain | |
| 239 0.03% 99.74% 1 301700 net.sf.samtools.BAMFileReader$BAMQueryFilteringIterator.advance | |
| 240 0.03% 99.76% 1 301701 sun.swing.SwingUtilities2.stringWidth | |
| 241 0.03% 99.79% 1 301702 net.sf.samtools.SAMRecord.getAlignmentEnd | |
| 242 0.03% 99.82% 1 301703 java.util.HashMap.containsKey | |
| 243 0.03% 99.84% 1 301704 java.awt.Component.repaint | |
| 244 0.03% 99.87% 1 301707 java.util.LinkedHashMap.get | |
| 245 0.03% 99.90% 1 301708 java.awt.geom.AffineTransform.translate | |
| 246 0.03% 99.92% 1 301709 java.util.zip.Inflater.reset | |
| 247 0.03% 99.95% 1 301710 org.broad.igv.feature.genome.GenomeImpl.getChromosome | |
| 248 0.03% 99.97% 1 301711 java.util.Arrays.mergeSort | |
| 249 0.03% 100.00% 1 301715 sun.java2d.pipe.ShapeSpanIterator.lineTo | |
| CPU SAMPLES END |
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| JAVA PROFILE 1.0.1, created Fri Jul 19 08:22:40 2013 | |
| Copyright (c) 2003, 2005, Oracle and/or its affiliates. All rights reserved. | |
| Redistribution and use in source and binary forms, with or without | |
| modification, are permitted provided that the following conditions | |
| are met: | |
| - Redistributions of source code must retain the above copyright | |
| notice, this list of conditions and the following disclaimer. | |
| - Redistributions in binary form must reproduce the above copyright | |
| notice, this list of conditions and the following disclaimer in the | |
| documentation and/or other materials provided with the distribution. | |
| - Neither the name of Oracle nor the names of its | |
| contributors may be used to endorse or promote products derived | |
| from this software without specific prior written permission. | |
| THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS | |
| IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, | |
| THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR | |
| PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR | |
| CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, | |
| EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, | |
| PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR | |
| PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF | |
| LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING | |
| NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS | |
| SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. | |
| Header for -agentlib:hprof (or -Xrunhprof) ASCII Output (JDK 5.0 JVMTI based) | |
| WARNING! This file format is under development, and is subject to | |
| change without notice. | |
| This file contains the following types of records: | |
| THREAD START | |
| THREAD END mark the lifetime of Java threads | |
| TRACE represents a Java stack trace. Each trace consists | |
| of a series of stack frames. Other records refer to | |
| TRACEs to identify (1) where object allocations have | |
| taken place, (2) the frames in which GC roots were | |
| found, and (3) frequently executed methods. | |
| HEAP DUMP is a complete snapshot of all live objects in the Java | |
| heap. Following distinctions are made: | |
| ROOT root set as determined by GC | |
| CLS classes | |
| OBJ instances | |
| ARR arrays | |
| SITES is a sorted list of allocation sites. This identifies | |
| the most heavily allocated object types, and the TRACE | |
| at which those allocations occurred. | |
| CPU SAMPLES is a statistical profile of program execution. The VM | |
| periodically samples all running threads, and assigns | |
| a quantum to active TRACEs in those threads. Entries | |
| in this record are TRACEs ranked by the percentage of | |
| total quanta they consumed; top-ranked TRACEs are | |
| typically hot spots in the program. | |
| CPU TIME is a profile of program execution obtained by measuring | |
| the time spent in individual methods (excluding the time | |
| spent in callees), as well as by counting the number of | |
| times each method is called. Entries in this record are | |
| TRACEs ranked by the percentage of total CPU time. The | |
| "count" field indicates the number of times each TRACE | |
| is invoked. | |
| MONITOR TIME is a profile of monitor contention obtained by measuring | |
| the time spent by a thread waiting to enter a monitor. | |
| Entries in this record are TRACEs ranked by the percentage | |
| of total monitor contention time and a brief description | |
| of the monitor. The "count" field indicates the number of | |
| times the monitor was contended at that TRACE. | |
| MONITOR DUMP is a complete snapshot of all the monitors and threads in | |
| the System. | |
| HEAP DUMP, SITES, CPU SAMPLES|TIME and MONITOR DUMP|TIME records are generated | |
| at program exit. They can also be obtained during program execution by typing | |
| Ctrl-\ (on Solaris) or by typing Ctrl-Break (on Win32). | |
| -------- | |
| THREAD START (obj=50000139, id = 200001, name="main", group="main") | |
| THREAD START (obj=50000379, id = 200004, name="Timer-0", group="main") | |
| THREAD START (obj=50000139, id = 200005, name="Java2D Disposer", group="system") | |
| THREAD START (obj=50000139, id = 200006, name="AWT-XAWT", group="main") | |
| THREAD START (obj=50000379, id = 200007, name="process reaper", group="main") | |
| THREAD END (id = 200007) | |
| THREAD START (obj=50000379, id = 200008, name="process reaper", group="main") | |
| THREAD END (id = 200008) | |
| THREAD START (obj=50000139, id = 200009, name="Image Fetcher 0", group="main") | |
| THREAD START (obj=50000139, id = 200010, name="AWT-Shutdown", group="main") | |
| THREAD START (obj=500009c6, id = 200011, name="AWT-EventQueue-0", group="main") | |
| THREAD START (obj=50000379, id = 200012, name="Timer-1", group="main") | |
| THREAD START (obj=50000139, id = 200013, name="TimerQueue", group="system") | |
| THREAD START (obj=50000139, id = 200014, name="Keep-Alive-Timer", group="system") | |
| THREAD START (obj=50000139, id = 200015, name="pool-1-thread-1", group="main") | |
| THREAD START (obj=50000139, id = 200016, name="pool-1-thread-2", group="main") | |
| THREAD START (obj=50000139, id = 200017, name="pool-1-thread-3", group="main") | |
| THREAD START (obj=50000139, id = 200018, name="pool-1-thread-4", group="main") | |
| THREAD START (obj=50000139, id = 200019, name="pool-1-thread-5", group="main") | |
| THREAD START (obj=50000139, id = 200020, name="Thread-6", group="main") | |
| THREAD START (obj=50000139, id = 200021, name="pool-1-thread-6", group="main") | |
| THREAD END (id = 200001) | |
| THREAD START (obj=50000139, id = 200022, name="DestroyJavaVM", group="main") | |
| THREAD START (obj=50000139, id = 200023, name="pool-1-thread-7", group="main") | |
| THREAD START (obj=50000139, id = 200024, name="pool-1-thread-8", group="main") | |
| THREAD START (obj=50000139, id = 200025, name="pool-1-thread-9", group="main") | |
| THREAD END (id = 200014) | |
| THREAD END (id = 200009) | |
| THREAD START (obj=50000139, id = 200026, name="pool-1-thread-10", group="main") | |
| THREAD START (obj=50000379, id = 200028, name="Thread-1", group="main") | |
| THREAD START (obj=50000379, id = 200027, name="Thread-2", group="main") | |
| THREAD END (id = 200028) | |
| THREAD START (obj=50000139, id = 200029, name="Thread-3", group="main") | |
| THREAD END (id = 200027) | |
| THREAD START (obj=50000139, id = 200030, name="Thread-4", group="system") | |
| THREAD END (id = 200030) | |
| THREAD END (id = 200004) | |
| THREAD END (id = 200020) | |
| THREAD END (id = 200029) | |
| THREAD END (id = 200021) | |
| TRACE 301784: | |
| java.net.PlainSocketImpl.socketAccept(PlainSocketImpl.java:Unknown line) | |
| java.net.AbstractPlainSocketImpl.accept(AbstractPlainSocketImpl.java:375) | |
| java.net.ServerSocket.implAccept(ServerSocket.java:470) | |
| TRACE 301951: | |
| sun.java2d.loops.MaskFill.FillAAPgram(MaskFill.java:Unknown line) | |
| sun.java2d.pipe.AlphaColorPipe.fillParallelogram(AlphaColorPipe.java:75) | |
| sun.java2d.pipe.PixelToParallelogramConverter.fillRectangle(PixelToParallelogramConverter.java:322) | |
| TRACE 300768: | |
| sun.awt.X11.XToolkit.waitForEvents(XToolkit.java:Unknown line) | |
| sun.awt.X11.XToolkit.run(XToolkit.java:568) | |
| sun.awt.X11.XToolkit.run(XToolkit.java:543) | |
| TRACE 301826: | |
| sun.java2d.loops.MaskFill.FillAAPgram(MaskFill.java:Unknown line) | |
| sun.java2d.pipe.AlphaColorPipe.fillParallelogram(AlphaColorPipe.java:75) | |
| sun.java2d.pipe.PixelToParallelogramConverter.drawGeneralLine(PixelToParallelogramConverter.java:287) | |
| TRACE 301956: | |
| sun.java2d.loops.MaskFill.DrawAAPgram(MaskFill.java:Unknown line) | |
| sun.java2d.pipe.AlphaColorPipe.drawParallelogram(AlphaColorPipe.java:87) | |
| sun.java2d.pipe.PixelToParallelogramConverter.drawRectangle(PixelToParallelogramConverter.java:374) | |
| TRACE 301953: | |
| sun.misc.Unsafe.unpark(Unsafe.java:Unknown line) | |
| java.util.concurrent.locks.LockSupport.unpark(LockSupport.java:152) | |
| java.util.concurrent.locks.AbstractQueuedSynchronizer.unparkSuccessor(AbstractQueuedSynchronizer.java:666) | |
| TRACE 301865: | |
| java.util.zip.Inflater.inflateBytes(Inflater.java:Unknown line) | |
| java.util.zip.Inflater.inflate(Inflater.java:255) | |
| net.sf.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:96) | |
| TRACE 301895: | |
| org.broad.igv.sam.DenseAlignmentCounts.incBlockCounts(DenseAlignmentCounts.java:324) | |
| org.broad.igv.sam.BaseAlignmentCounts.incCounts(BaseAlignmentCounts.java:114) | |
| org.broad.igv.sam.AlignmentTileLoader$AlignmentTile.addRecord(AlignmentTileLoader.java:337) | |
| TRACE 301965: | |
| sun.awt.X11.XlibWrapper.XEventsQueued(XlibWrapper.java:Unknown line) | |
| sun.awt.X11.XToolkit.run(XToolkit.java:565) | |
| sun.awt.X11.XToolkit.run(XToolkit.java:543) | |
| TRACE 301901: | |
| org.broad.igv.sam.SamAlignment.getFileSource(SamAlignment.java:637) | |
| org.broad.igv.sam.SamAlignment.finish(SamAlignment.java:794) | |
| org.broad.igv.sam.AlignmentTileLoader$AlignmentTile.addRecord(AlignmentTileLoader.java:357) | |
| TRACE 301968: | |
| sun.java2d.loops.MaskFill.MaskFill(MaskFill.java:Unknown line) | |
| sun.java2d.pipe.AlphaColorPipe.renderPathTile(AlphaColorPipe.java:55) | |
| sun.java2d.pipe.AAShapePipe.renderTiles(AAShapePipe.java:201) | |
| TRACE 301898: | |
| net.sf.samtools.SAMRecord.getFileSource(SAMRecord.java:1664) | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:138) | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:43) | |
| TRACE 301896: | |
| org.broad.igv.sam.BisulfiteCounts.incrementCounts(BisulfiteCounts.java:81) | |
| org.broad.igv.sam.BaseAlignmentCounts.incCounts(BaseAlignmentCounts.java:91) | |
| org.broad.igv.sam.AlignmentTileLoader$AlignmentTile.addRecord(AlignmentTileLoader.java:337) | |
| TRACE 300020: | |
| java.lang.String.intern(String.java:Unknown line) | |
| java.util.jar.Attributes$Name.<init>(Attributes.java:466) | |
| java.util.jar.Attributes.putValue(Attributes.java:168) | |
| TRACE 301891: | |
| org.broad.igv.sam.SamAlignment.getFileSource(SamAlignment.java:637) | |
| org.broad.igv.sam.SamAlignment.finish(SamAlignment.java:794) | |
| org.broad.igv.sam.AlignmentTileLoader$AlignmentTile.addRecord(AlignmentTileLoader.java:357) | |
| TRACE 301871: | |
| net.sf.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:251) | |
| java.io.DataInputStream.read(DataInputStream.java:149) | |
| net.sf.samtools.util.BinaryCodec.readBytesOrFewer(BinaryCodec.java:394) | |
| TRACE 301912: | |
| net.sf.samtools.SAMRecord.getFileSource(SAMRecord.java:1664) | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:138) | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:43) | |
| TRACE 300031: | |
| java.util.zip.Inflater.inflateBytes(Inflater.java:Unknown line) | |
| java.util.zip.Inflater.inflate(Inflater.java:255) | |
| java.util.zip.InflaterInputStream.read(InflaterInputStream.java:152) | |
| TRACE 301824: | |
| sun.awt.X11.XlibWrapper.XEventsQueued(XlibWrapper.java:Unknown line) | |
| sun.awt.X11.XToolkit.run(XToolkit.java:565) | |
| sun.awt.X11.XToolkit.run(XToolkit.java:543) | |
| TRACE 301911: | |
| java.nio.ByteBuffer.get(ByteBuffer.java:692) | |
| net.sf.samtools.BinaryTagCodec.readNullTerminatedString(BinaryTagCodec.java:417) | |
| net.sf.samtools.BinaryTagCodec.readSingleValue(BinaryTagCodec.java:318) | |
| TRACE 301969: | |
| sun.java2d.loops.MaskFill.FillAAPgram(MaskFill.java:Unknown line) | |
| sun.java2d.pipe.AlphaColorPipe.fillParallelogram(AlphaColorPipe.java:75) | |
| sun.java2d.pipe.PixelToParallelogramConverter.fillOuterParallelogram(PixelToParallelogramConverter.java:426) | |
| TRACE 301979: | |
| java.lang.StrictMath.ceil(StrictMath.java:Unknown line) | |
| java.lang.Math.ceil(Math.java:405) | |
| org.broad.igv.sam.AlignmentRenderer.drawAlignment(AlignmentRenderer.java:525) | |
| TRACE 301974: | |
| sun.misc.Unsafe.park(Unsafe.java:Unknown line) | |
| java.util.concurrent.locks.LockSupport.park(LockSupport.java:186) | |
| java.util.concurrent.locks.AbstractQueuedSynchronizer.parkAndCheckInterrupt(AbstractQueuedSynchronizer.java:838) | |
| TRACE 302030: | |
| sun.java2d.loops.DrawGlyphListAA.DrawGlyphListAA(DrawGlyphListAA.java:Unknown line) | |
| sun.java2d.pipe.AATextRenderer.drawGlyphList(AATextRenderer.java:41) | |
| sun.java2d.pipe.GlyphListPipe.drawString(GlyphListPipe.java:72) | |
| TRACE 301864: | |
| net.sf.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:378) | |
| net.sf.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:365) | |
| net.sf.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:113) | |
| TRACE 301906: | |
| java.util.Hashtable.get(Hashtable.java:351) | |
| org.broad.igv.PreferenceManager.getAsBoolean(PreferenceManager.java:293) | |
| org.broad.igv.sam.SamAlignment.createAlignmentBlocks(SamAlignment.java:331) | |
| TRACE 300301: | |
| sun.nio.cs.UTF_8.updatePositions(UTF_8.java:76) | |
| sun.nio.cs.UTF_8$Decoder.xflow(UTF_8.java:183) | |
| sun.nio.cs.UTF_8$Decoder.decodeArrayLoop(UTF_8.java:260) | |
| TRACE 301827: | |
| java.security.AccessController.doPrivileged(AccessController.java:Unknown line) | |
| javax.swing.Timer.post(Timer.java:612) | |
| javax.swing.TimerQueue.run(TimerQueue.java:177) | |
| TRACE 301930: | |
| java.util.HashMap.getEntry(HashMap.java:361) | |
| java.util.LinkedHashMap.get(LinkedHashMap.java:297) | |
| org.broad.igv.util.ObjectCache.get(ObjectCache.java:72) | |
| TRACE 302017: | |
| org.broad.igv.sam.AlignmentTileLoader$AlignmentTile.addRecord(AlignmentTileLoader.java:352) | |
| org.broad.igv.sam.AlignmentTileLoader.loadTile(AlignmentTileLoader.java:168) | |
| org.broad.igv.sam.AlignmentDataManager.loadInterval(AlignmentDataManager.java:364) | |
| TRACE 300017: | |
| java.lang.StringCoding$StringDecoder.decode(StringCoding.java:151) | |
| java.lang.StringCoding.decode(StringCoding.java:191) | |
| java.lang.String.<init>(String.java:451) | |
| TRACE 300256: | |
| sun.security.provider.DigestBase.engineUpdate(DigestBase.java:139) | |
| java.security.MessageDigest$Delegate.engineUpdate(MessageDigest.java:555) | |
| java.security.MessageDigest.update(MessageDigest.java:300) | |
| TRACE 300777: | |
| java.io.FileInputStream.readBytes(FileInputStream.java:Unknown line) | |
| java.io.FileInputStream.read(FileInputStream.java:236) | |
| java.io.BufferedInputStream.read1(BufferedInputStream.java:273) | |
| TRACE 300778: | |
| java.lang.UNIXProcess.waitForProcessExit(UNIXProcess.java:Unknown line) | |
| java.lang.UNIXProcess.access$900(UNIXProcess.java:36) | |
| java.lang.UNIXProcess$1$1.run(UNIXProcess.java:148) | |
| TRACE 301755: | |
| java.net.SocketInputStream.socketRead0(SocketInputStream.java:Unknown line) | |
| java.net.SocketInputStream.read(SocketInputStream.java:146) | |
| java.io.BufferedInputStream.fill(BufferedInputStream.java:235) | |
| TRACE 301870: | |
| net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:522) | |
| net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:481) | |
| net.sf.samtools.BAMFileReader$BAMQueryFilteringIterator.advance(BAMFileReader.java:750) | |
| TRACE 301905: | |
| java.util.HashMap.get(HashMap.java:317) | |
| org.broad.igv.sam.AlignmentTrack.getBisulfiteContextPreContext(AlignmentTrack.java:880) | |
| org.broad.igv.sam.BisulfiteCounts.contextIsMatching(BisulfiteCounts.java:143) | |
| TRACE 301925: | |
| java.io.RandomAccessFile.readBytes(RandomAccessFile.java:Unknown line) | |
| java.io.RandomAccessFile.read(RandomAccessFile.java:355) | |
| net.sf.samtools.seekablestream.SeekableFileStream.read(SeekableFileStream.java:77) | |
| TRACE 301967: | |
| sun.java2d.x11.X11SurfaceData.XSetForeground(X11SurfaceData.java:Unknown line) | |
| sun.java2d.x11.X11SurfaceData.getGC(X11SurfaceData.java:649) | |
| sun.java2d.x11.X11SurfaceData.getRenderGC(X11SurfaceData.java:599) | |
| TRACE 302015: | |
| java.lang.Integer.parseInt(Integer.java:514) | |
| org.broad.igv.sam.SamAlignment.createAlignmentBlocks(SamAlignment.java:360) | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:183) | |
| TRACE 301733: | |
| java.net.Inet6AddressImpl.lookupAllHostAddr(Inet6AddressImpl.java:Unknown line) | |
| java.net.InetAddress$1.lookupAllHostAddr(InetAddress.java:867) | |
| java.net.InetAddress.getAddressFromNameService(InetAddress.java:1246) | |
| TRACE 301808: | |
| java.util.HashMap.transfer(HashMap.java:501) | |
| java.util.HashMap.resize(HashMap.java:480) | |
| java.util.HashMap.addEntry(HashMap.java:772) | |
| TRACE 301861: | |
| net.sf.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:199) | |
| net.sf.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:558) | |
| net.sf.samtools.BAMFileReader$BAMFileIndexIterator.getNextRecord(BAMFileReader.java:665) | |
| TRACE 301893: | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:43) | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:26) | |
| org.broad.igv.sam.AlignmentTileLoader.loadTile(AlignmentTileLoader.java:126) | |
| TRACE 301899: | |
| java.util.Hashtable.get(Hashtable.java:354) | |
| org.broad.igv.PreferenceManager.getAsBoolean(PreferenceManager.java:293) | |
| org.broad.igv.sam.SamAlignment.createAlignmentBlocks(SamAlignment.java:331) | |
| TRACE 301902: | |
| org.broad.igv.sam.SamAlignment.createAlignmentBlocks(SamAlignment.java:353) | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:183) | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:43) | |
| TRACE 301908: | |
| java.lang.Integer.toString(Integer.java:329) | |
| java.lang.Integer.toString(Integer.java:134) | |
| java.lang.String.valueOf(String.java:2943) | |
| TRACE 301915: | |
| org.broad.igv.sam.SamAlignment.createAlignmentBlocks(SamAlignment.java:515) | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:183) | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:43) | |
| TRACE 301918: | |
| org.broad.igv.sam.BisulfiteCounts.positionMatchesContext(BisulfiteCounts.java:184) | |
| org.broad.igv.sam.BisulfiteCounts.contextIsMatching(BisulfiteCounts.java:157) | |
| org.broad.igv.sam.BisulfiteCounts.incrementCounts(BisulfiteCounts.java:83) | |
| TRACE 301923: | |
| net.sf.samtools.BinaryCigarCodec.decode(BinaryCigarCodec.java:74) | |
| net.sf.samtools.BAMRecord.getCigar(BAMRecord.java:243) | |
| net.sf.samtools.SAMRecord.getAlignmentEnd(SAMRecord.java:456) | |
| TRACE 302020: | |
| org.broad.igv.sam.SamAlignment.createAlignmentBlocks(SamAlignment.java:350) | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:183) | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:43) | |
| TRACE 302024: | |
| net.sf.samtools.BinaryTagCodec.readTags(BinaryTagCodec.java:303) | |
| net.sf.samtools.BAMRecord.decodeAttributes(BAMRecord.java:308) | |
| net.sf.samtools.BAMRecord.getAttribute(BAMRecord.java:288) | |
| TRACE 300016: | |
| java.util.HashMap.<init>(HashMap.java:204) | |
| java.util.HashMap.<init>(HashMap.java:216) | |
| java.util.jar.Attributes.<init>(Attributes.java:74) | |
| TRACE 300274: | |
| java.lang.ClassLoader.defineClass1(ClassLoader.java:Unknown line) | |
| java.lang.ClassLoader.defineClass(ClassLoader.java:634) | |
| java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142) | |
| TRACE 301653: | |
| sun.awt.X11.XlibWrapper.XGetWindowAttributes(XlibWrapper.java:Unknown line) | |
| sun.awt.X11.XWM.syncTopLevelPos(XWM.java:1488) | |
| sun.awt.X11.XWM.getInsets(XWM.java:1599) | |
| TRACE 301654: | |
| sun.awt.X11.XlibWrapper.XSync(XlibWrapper.java:Unknown line) | |
| sun.awt.X11.XToolkit.XSync(XToolkit.java:1174) | |
| sun.awt.X11.XWM.syncTopLevelPos(XWM.java:1493) | |
| TRACE 301873: | |
| org.broad.igv.sam.SamAlignment.setPairOrientation(SamAlignment.java:236) | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:165) | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:43) | |
| TRACE 301880: | |
| org.broad.igv.feature.genome.SequenceWrapper.getSequence(SequenceWrapper.java:88) | |
| org.broad.igv.feature.genome.Genome.getSequence(Genome.java:408) | |
| org.broad.igv.sam.BisulfiteCounts.incrementCounts(BisulfiteCounts.java:51) | |
| TRACE 301884: | |
| net.sf.samtools.BAMRecord.decodeBaseQualities(BAMRecord.java:317) | |
| net.sf.samtools.BAMRecord.getBaseQualities(BAMRecord.java:279) | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:183) | |
| TRACE 301903: | |
| net.sf.samtools.SAMBinaryTagAndValue.find(SAMBinaryTagAndValue.java:119) | |
| net.sf.samtools.SAMRecord.getAttribute(SAMRecord.java:1083) | |
| net.sf.samtools.BAMRecord.getAttribute(BAMRecord.java:290) | |
| TRACE 301909: | |
| java.util.HashMap.getEntry(HashMap.java:361) | |
| java.util.LinkedHashMap.get(LinkedHashMap.java:297) | |
| org.broad.igv.feature.genome.Genome.getChromosome(Genome.java:269) | |
| TRACE 301922: | |
| net.sf.samtools.SAMReadGroupRecord.getPlatform(SAMReadGroupRecord.java:75) | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:174) | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:43) | |
| TRACE 301927: | |
| java.lang.StringBuilder.append(StringBuilder.java:136) | |
| org.broad.igv.feature.genome.SequenceWrapper.getKey(SequenceWrapper.java:162) | |
| org.broad.igv.feature.genome.SequenceWrapper.getSequenceTile(SequenceWrapper.java:141) | |
| TRACE 302010: | |
| net.sf.samtools.util.StringUtil.bytesToString(StringUtil.java:301) | |
| net.sf.samtools.util.StringUtil.bytesToString(StringUtil.java:288) | |
| net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:205) | |
| TRACE 300001: | |
| java.lang.ClassLoader.findBootstrapClass(ClassLoader.java:Unknown line) | |
| java.lang.ClassLoader.findBootstrapClass0(ClassLoader.java:900) | |
| java.lang.ClassLoader.loadClass(ClassLoader.java:316) | |
| TRACE 300275: | |
| sun.security.util.ManifestEntryVerifier.update(ManifestEntryVerifier.java:165) | |
| java.util.jar.JarVerifier.update(JarVerifier.java:202) | |
| java.util.jar.JarVerifier$VerifierStream.read(JarVerifier.java:425) | |
| TRACE 300294: | |
| java.util.zip.ZipFile.getEntry(ZipFile.java:Unknown line) | |
| java.util.zip.ZipFile.getEntry(ZipFile.java:166) | |
| java.util.jar.JarFile.getEntry(JarFile.java:223) | |
| TRACE 300576: | |
| sun.awt.X11GraphicsEnvironment.initDisplay(X11GraphicsEnvironment.java:Unknown line) | |
| sun.awt.X11GraphicsEnvironment.access$200(X11GraphicsEnvironment.java:62) | |
| sun.awt.X11GraphicsEnvironment$1.run(X11GraphicsEnvironment.java:178) | |
| TRACE 301029: | |
| java.lang.System.arraycopy(System.java:Unknown line) | |
| java.io.ByteArrayOutputStream.write(ByteArrayOutputStream.java:113) | |
| java.io.DataOutputStream.write(DataOutputStream.java:107) | |
| TRACE 301676: | |
| sun.awt.X11.XlibWrapper.XGetIconSizes(XlibWrapper.java:Unknown line) | |
| sun.awt.X11.XIconWindow.getIconSizes(XIconWindow.java:66) | |
| sun.awt.X11.XIconWindow.calcIconSize(XIconWindow.java:97) | |
| TRACE 301734: | |
| sun.awt.X11.XInputMethod.openXIMNative(XInputMethod.java:Unknown line) | |
| sun.awt.X11.XInputMethod.openXIM(XInputMethod.java:62) | |
| sun.awt.X11InputMethod.initXIM(X11InputMethod.java:202) | |
| TRACE 301875: | |
| sun.misc.Unsafe.compareAndSwapLong(Unsafe.java:Unknown line) | |
| java.util.concurrent.atomic.AtomicLong.compareAndSet(AtomicLong.java:149) | |
| java.util.Random.next(Random.java:154) | |
| TRACE 301877: | |
| java.lang.System.arraycopy(System.java:Unknown line) | |
| java.nio.HeapByteBuffer.get(HeapByteBuffer.java:146) | |
| java.nio.ByteBuffer.get(ByteBuffer.java:692) | |
| TRACE 301904: | |
| net.sf.samtools.BAMRecord.decodeAttributes(BAMRecord.java:308) | |
| net.sf.samtools.BAMRecord.getAttribute(BAMRecord.java:288) | |
| net.sf.samtools.SAMRecord.getAttribute(SAMRecord.java:891) | |
| TRACE 301916: | |
| org.broad.igv.feature.genome.Genome.getSequence(Genome.java:408) | |
| org.broad.igv.sam.BisulfiteCounts.incrementCounts(BisulfiteCounts.java:51) | |
| org.broad.igv.sam.BaseAlignmentCounts.incCounts(BaseAlignmentCounts.java:91) | |
| TRACE 301921: | |
| net.sf.samtools.BAMRecord.getCigar(BAMRecord.java:241) | |
| net.sf.samtools.SAMRecord.getAlignmentEnd(SAMRecord.java:456) | |
| net.sf.samtools.BAMFileReader$BAMQueryFilteringIterator.advance(BAMFileReader.java:772) | |
| TRACE 301932: | |
| org.broad.igv.feature.genome.Genome.getChromosome(Genome.java:269) | |
| org.broad.igv.feature.genome.Genome.getSequence(Genome.java:400) | |
| org.broad.igv.sam.BisulfiteCounts.incrementCounts(BisulfiteCounts.java:51) | |
| TRACE 301976: | |
| java.lang.StrictMath.ceil(StrictMath.java:Unknown line) | |
| java.lang.Math.ceil(Math.java:405) | |
| sun.java2d.pisces.Renderer.somethingTo(Renderer.java:555) | |
| TRACE 302011: | |
| org.broad.igv.sam.AlignmentTrack.getBisulfiteContextPreContext(AlignmentTrack.java:880) | |
| org.broad.igv.sam.BisulfiteCounts.contextIsMatching(BisulfiteCounts.java:143) | |
| org.broad.igv.sam.BisulfiteCounts.incrementCounts(BisulfiteCounts.java:83) | |
| TRACE 302012: | |
| org.broad.igv.sam.BisulfiteCounts.incrementCounts(BisulfiteCounts.java:34) | |
| org.broad.igv.sam.BaseAlignmentCounts.incCounts(BaseAlignmentCounts.java:91) | |
| org.broad.igv.sam.AlignmentTileLoader$AlignmentTile.addRecord(AlignmentTileLoader.java:337) | |
| TRACE 302018: | |
| org.broad.igv.util.ObjectCache.put(ObjectCache.java:57) | |
| org.broad.igv.sam.AlignmentTileLoader.loadTile(AlignmentTileLoader.java:138) | |
| org.broad.igv.sam.AlignmentDataManager.loadInterval(AlignmentDataManager.java:364) | |
| TRACE 302022: | |
| net.sf.samtools.SAMBinaryTagAndValue.insert(SAMBinaryTagAndValue.java:101) | |
| net.sf.samtools.SAMBinaryTagAndValue.insert(SAMBinaryTagAndValue.java:101) | |
| net.sf.samtools.BinaryTagCodec.readTags(BinaryTagCodec.java:301) | |
| TRACE 302051: | |
| net.sf.samtools.util.StringUtil.bytesToString(StringUtil.java:301) | |
| net.sf.samtools.util.StringUtil.bytesToString(StringUtil.java:288) | |
| net.sf.samtools.BinaryTagCodec.readNullTerminatedString(BinaryTagCodec.java:420) | |
| TRACE 300018: | |
| java.util.jar.Manifest.read(Manifest.java:235) | |
| java.util.jar.Manifest.<init>(Manifest.java:69) | |
| java.util.jar.JarFile.getManifestFromReference(JarFile.java:177) | |
| TRACE 300061: | |
| java.util.regex.Pattern$CharPropertyNames.defCtype(Pattern.java:5096) | |
| java.util.regex.Pattern$CharPropertyNames.<clinit>(Pattern.java:5201) | |
| java.util.regex.Pattern.charPropertyNodeFor(Pattern.java:2452) | |
| TRACE 300104: | |
| java.util.Arrays.copyOfRange(Arrays.java:3221) | |
| java.lang.String.<init>(String.java:233) | |
| java.lang.StringBuilder.toString(StringBuilder.java:447) | |
| TRACE 300105: | |
| java.util.Arrays.copyOf(Arrays.java:2894) | |
| java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.java:117) | |
| java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:407) | |
| TRACE 300106: | |
| sun.security.util.ManifestDigester.<init>(ManifestDigester.java:140) | |
| java.util.jar.JarVerifier.processEntry(JarVerifier.java:267) | |
| java.util.jar.JarVerifier.update(JarVerifier.java:205) | |
| TRACE 300132: | |
| java.lang.Class.forName0(Class.java:Unknown line) | |
| java.lang.Class.forName(Class.java:186) | |
| java.security.Provider$Service.getImplClass(Provider.java:1277) | |
| TRACE 300161: | |
| sun.security.x509.CertificateX509Key.<init>(CertificateX509Key.java:75) | |
| sun.security.x509.X509CertInfo.parse(X509CertInfo.java:705) | |
| sun.security.x509.X509CertInfo.<init>(X509CertInfo.java:169) | |
| TRACE 300210: | |
| sun.text.normalizer.NormalizerBase.<clinit>(NormalizerBase.java:287) | |
| java.text.Normalizer.normalize(Normalizer.java:164) | |
| sun.security.x509.AVA.toRFC2253CanonicalString(AVA.java:1003) | |
| TRACE 300248: | |
| sun.security.provider.SHA.implCompress(SHA.java:122) | |
| sun.security.provider.DigestBase.engineUpdate(DigestBase.java:139) | |
| java.security.MessageDigest$Delegate.engineUpdate(MessageDigest.java:555) | |
| TRACE 300249: | |
| sun.misc.Unsafe.getInt(Unsafe.java:Unknown line) | |
| sun.security.provider.ByteArrayAccess.b2iBig64(ByteArrayAccess.java:256) | |
| sun.security.provider.SHA.implCompress(SHA.java:122) | |
| TRACE 300250: | |
| sun.security.provider.DigestBase.engineUpdate(DigestBase.java:140) | |
| java.security.MessageDigest$Delegate.engineUpdate(MessageDigest.java:555) | |
| java.security.MessageDigest.update(MessageDigest.java:300) | |
| TRACE 300259: | |
| java.util.Hashtable.put(Hashtable.java:416) | |
| sun.security.util.SignatureFileVerifier.updateSigners(SignatureFileVerifier.java:646) | |
| sun.security.util.SignatureFileVerifier.processImpl(SignatureFileVerifier.java:258) | |
| TRACE 300297: | |
| java.util.HashMap.<init>(HashMap.java:240) | |
| java.util.jar.Attributes.<init>(Attributes.java:84) | |
| java.util.jar.Attributes.clone(Attributes.java:291) | |
| TRACE 300298: | |
| java.util.HashMap$HashIterator.<init>(HashMap.java:796) | |
| java.util.HashMap$EntryIterator.<init>(HashMap.java:849) | |
| java.util.HashMap$EntryIterator.<init>(HashMap.java:849) | |
| TRACE 300300: | |
| java.util.jar.JarFile.getBytes(JarFile.java:375) | |
| java.util.jar.JarFile.initializeVerifier(JarFile.java:334) | |
| java.util.jar.JarFile.getInputStream(JarFile.java:403) | |
| TRACE 300302: | |
| java.util.Hashtable.rehash(Hashtable.java:387) | |
| java.util.Hashtable.put(Hashtable.java:429) | |
| sun.security.util.SignatureFileVerifier.updateSigners(SignatureFileVerifier.java:646) | |
| TRACE 300310: | |
| java.beans.Introspector.instantiate(Introspector.java:1488) | |
| java.beans.Introspector.findExplicitBeanInfo(Introspector.java:446) | |
| java.beans.Introspector.<init>(Introspector.java:395) | |
| TRACE 300367: | |
| java.lang.Package.getSystemPackage(Package.java:512) | |
| java.lang.ClassLoader.getPackage(ClassLoader.java:1447) | |
| java.lang.ClassLoader.getPackage(ClassLoader.java:1445) | |
| TRACE 300439: | |
| com.sun.org.apache.xerces.internal.parsers.XML11Configuration.<init>(XML11Configuration.java:541) | |
| com.sun.org.apache.xerces.internal.parsers.XIncludeAwareParserConfiguration.<init>(XIncludeAwareParserConfiguration.java:128) | |
| com.sun.org.apache.xerces.internal.parsers.XIncludeAwareParserConfiguration.<init>(XIncludeAwareParserConfiguration.java:89) | |
| TRACE 300501: | |
| com.sun.org.apache.xerces.internal.dom.DeferredDocumentImpl.getNodeObject(DeferredDocumentImpl.java:957) | |
| com.sun.org.apache.xerces.internal.dom.DeferredElementDefinitionImpl.synchronizeChildren(DeferredElementDefinitionImpl.java:117) | |
| com.sun.org.apache.xerces.internal.dom.ParentNode.setReadOnly(ParentNode.java:905) | |
| TRACE 300551: | |
| javax.swing.UIManager$LAFState.<init>(UIManager.java:188) | |
| javax.swing.UIManager$LAFState.<init>(UIManager.java:185) | |
| javax.swing.UIManager.getLAFState(UIManager.java:245) | |
| TRACE 300618: | |
| sun.font.FontManager.getFCLocaleStr(FontManager.java:3110) | |
| sun.font.FontManager.initFontConfigFonts(FontManager.java:3190) | |
| sun.font.FontManager.getDefaultPlatformFont(FontManager.java:3336) | |
| TRACE 300658: | |
| sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:167) | |
| sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:272) | |
| sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:324) | |
| TRACE 300700: | |
| sun.java2d.SurfaceData.<clinit>(SurfaceData.java:448) | |
| sun.awt.X11GraphicsConfig.<clinit>(X11GraphicsConfig.java:76) | |
| sun.awt.X11GraphicsDevice.makeDefaultConfiguration(X11GraphicsDevice.java:263) | |
| TRACE 300746: | |
| sun.awt.X11.XlibWrapper.XKeysymToKeycode(XlibWrapper.java:Unknown line) | |
| sun.awt.X11.XToolkit.keysymToPrimaryKeycode(XToolkit.java:1542) | |
| sun.awt.X11.XToolkit.setupModifierMap(XToolkit.java:1560) | |
| TRACE 300767: | |
| javax.naming.CompositeName.<init>(CompositeName.java:231) | |
| org.GNOME.Accessibility.AccessibleFactory.<clinit>(AccessibleFactory.java:32) | |
| org.GNOME.Accessibility.JavaBridge.<clinit>(JavaBridge.java:63) | |
| TRACE 300776: | |
| java.lang.UNIXProcess.forkAndExec(UNIXProcess.java:Unknown line) | |
| java.lang.UNIXProcess.access$500(UNIXProcess.java:36) | |
| java.lang.UNIXProcess$1$1.run(UNIXProcess.java:125) | |
| TRACE 300806: | |
| javax.swing.UIManager.initialize(UIManager.java:1460) | |
| javax.swing.UIManager.maybeInitialize(UIManager.java:1395) | |
| javax.swing.UIManager.getDefaults(UIManager.java:644) | |
| TRACE 300829: | |
| java.util.zip.InflaterInputStream.<init>(InflaterInputStream.java:112) | |
| java.util.zip.ZipFile$1.<init>(ZipFile.java:229) | |
| java.util.zip.ZipFile.getInputStream(ZipFile.java:229) | |
| TRACE 300880: | |
| sun.awt.image.PNGImageDecoder.<clinit>(PNGImageDecoder.java:764) | |
| sun.awt.image.InputStreamImageSource.getDecoder(InputStreamImageSource.java:242) | |
| sun.awt.image.URLImageSource.getDecoder(URLImageSource.java:158) | |
| TRACE 300895: | |
| com.jidesoft.plaf.LookAndFeelFactory.installJideExtension(LookAndFeelFactory.java:809) | |
| com.jidesoft.plaf.LookAndFeelFactory.installJideExtension(LookAndFeelFactory.java:633) | |
| com.jidesoft.plaf.LookAndFeelFactory.installJideExtension(LookAndFeelFactory.java:598) | |
| TRACE 300965: | |
| java.awt.image.ColorModel.getLinearRGB16TosRGB8LUT(ColorModel.java:1755) | |
| java.awt.image.ColorModel.getGray16TosRGB8LUT(ColorModel.java:1884) | |
| java.awt.image.ComponentColorModel.setupLUTs(ComponentColorModel.java:443) | |
| TRACE 300966: | |
| java.lang.StrictMath.floor(StrictMath.java:Unknown line) | |
| java.lang.Math.floor(Math.java:424) | |
| java.lang.Math.round(Math.java:652) | |
| TRACE 300969: | |
| java.io.RandomAccessFile.readBytes(RandomAccessFile.java:Unknown line) | |
| java.io.RandomAccessFile.read(RandomAccessFile.java:355) | |
| java.io.RandomAccessFile.readFully(RandomAccessFile.java:414) | |
| TRACE 300971: | |
| sun.security.ssl.SunJSSE.registerAlgorithms(SunJSSE.java:149) | |
| sun.security.ssl.SunJSSE.<init>(SunJSSE.java:112) | |
| com.sun.net.ssl.internal.ssl.Provider.<init>(Provider.java:41) | |
| TRACE 300989: | |
| org.broad.igv.ui.IGV.<init>(IGV.java:209) | |
| org.broad.igv.ui.IGV.createInstance(IGV.java:165) | |
| org.broad.igv.ui.Main.open(Main.java:159) | |
| TRACE 301003: | |
| java.util.zip.ZipFile.freeEntry(ZipFile.java:Unknown line) | |
| java.util.zip.ZipFile.access$800(ZipFile.java:46) | |
| java.util.zip.ZipFile$ZipFileInputStream.close(ZipFile.java:509) | |
| TRACE 301005: | |
| java.lang.Throwable.fillInStackTrace(Throwable.java:Unknown line) | |
| java.lang.Throwable.<init>(Throwable.java:198) | |
| java.lang.Exception.<init>(Exception.java:46) | |
| TRACE 301006: | |
| java.util.zip.ZipEntry.initFields(ZipEntry.java:Unknown line) | |
| java.util.zip.ZipEntry.<init>(ZipEntry.java:103) | |
| java.util.zip.ZipFile.getEntry(ZipFile.java:168) | |
| TRACE 301042: | |
| sun.awt.image.GifImageDecoder.parseImage(GifImageDecoder.java:Unknown line) | |
| sun.awt.image.GifImageDecoder.readImage(GifImageDecoder.java:596) | |
| sun.awt.image.GifImageDecoder.produceImage(GifImageDecoder.java:212) | |
| TRACE 301051: | |
| sun.awt.X11.XlibWrapper.XAllocColor(XlibWrapper.java:Unknown line) | |
| sun.awt.X11.XCustomCursor.createCursor(XCustomCursor.java:101) | |
| sun.awt.X11CustomCursor.createNativeCursor(X11CustomCursor.java:170) | |
| TRACE 301099: | |
| java.awt.datatransfer.DataFlavor.<clinit>(DataFlavor.java:183) | |
| sun.awt.datatransfer.DataTransferer.<clinit>(DataTransferer.java:236) | |
| java.awt.datatransfer.SystemFlavorMap.parseAndStoreReader(SystemFlavorMap.java:344) | |
| TRACE 301121: | |
| javax.swing.AbstractButton.updateDisplayedMnemonicIndex(AbstractButton.java:1656) | |
| javax.swing.AbstractButton.setModel(AbstractButton.java:1768) | |
| javax.swing.JButton.<init>(JButton.java:130) | |
| TRACE 301203: | |
| javax.swing.text.AbstractDocument.<init>(AbstractDocument.java:109) | |
| javax.swing.text.PlainDocument.<init>(PlainDocument.java:91) | |
| javax.swing.text.PlainDocument.<init>(PlainDocument.java:81) | |
| TRACE 301239: | |
| javax.swing.AbstractButton.addChangeListener(AbstractButton.java:1866) | |
| com.jidesoft.plaf.basic.BasicJideButtonUI.installListeners(BasicJideButtonUI.java:169) | |
| com.jidesoft.plaf.basic.BasicJideButtonUI.installUI(BasicJideButtonUI.java:80) | |
| TRACE 301245: | |
| java.lang.Class$MethodArray.addIfNotPresent(Class.java:2485) | |
| java.lang.Class$MethodArray.addAllIfNotPresent(Class.java:2497) | |
| java.lang.Class.privateGetPublicMethods(Class.java:2601) | |
| TRACE 301246: | |
| java.lang.reflect.Array.newArray(Array.java:Unknown line) | |
| java.lang.reflect.Array.newInstance(Array.java:70) | |
| java.util.Arrays.copyOf(Arrays.java:2772) | |
| TRACE 301247: | |
| java.util.concurrent.locks.AbstractQueuedSynchronizer.compareAndSetState(AbstractQueuedSynchronizer.java:570) | |
| java.util.concurrent.locks.ReentrantLock$NonfairSync.lock(ReentrantLock.java:211) | |
| java.util.concurrent.locks.ReentrantLock.lock(ReentrantLock.java:290) | |
| TRACE 301248: | |
| java.lang.Throwable.fillInStackTrace(Throwable.java:Unknown line) | |
| java.lang.Throwable.<init>(Throwable.java:213) | |
| java.lang.Exception.<init>(Exception.java:58) | |
| TRACE 301249: | |
| java.util.ArrayList.<init>(ArrayList.java:132) | |
| sun.reflect.generics.parser.SignatureParser.parseClassTypeSignature(SignatureParser.java:259) | |
| sun.reflect.generics.parser.SignatureParser.parseFieldTypeSignature(SignatureParser.java:246) | |
| TRACE 301252: | |
| sun.reflect.ByteVectorImpl.<init>(ByteVectorImpl.java:37) | |
| sun.reflect.ByteVectorImpl.<init>(ByteVectorImpl.java:33) | |
| sun.reflect.ByteVectorFactory.create(ByteVectorFactory.java:30) | |
| TRACE 301254: | |
| sun.misc.Resource.getBytes(Resource.java:124) | |
| java.net.URLClassLoader.defineClass(URLClassLoader.java:273) | |
| java.net.URLClassLoader.access$000(URLClassLoader.java:73) | |
| TRACE 301257: | |
| com.jidesoft.swing.JideSplitPane.createSplitPaneDivider(JideSplitPane.java:1052) | |
| com.jidesoft.swing.JideSplitPane.addExtraDividers(JideSplitPane.java:958) | |
| com.jidesoft.swing.JideSplitPane.componentAdded(JideSplitPane.java:787) | |
| TRACE 301259: | |
| java.lang.Class.newInstance0(Class.java:362) | |
| java.lang.Class.newInstance(Class.java:325) | |
| java.security.Provider$Service.newInstance(Provider.java:1238) | |
| TRACE 301274: | |
| java.lang.Object.getClass(Object.java:Unknown line) | |
| javax.swing.UIDefaults.getUI(UIDefaults.java:753) | |
| javax.swing.UIManager.getUI(UIManager.java:1000) | |
| TRACE 301280: | |
| java.lang.Object.clone(Object.java:Unknown line) | |
| com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.getRecognizedProperties(XMLErrorReporter.java:513) | |
| com.sun.org.apache.xerces.internal.parsers.XML11Configuration.addRecognizedParamsAndSetDefaults(XML11Configuration.java:1473) | |
| TRACE 301285: | |
| com.sun.org.apache.xerces.internal.impl.dtd.XMLSimpleType.setValues(XMLSimpleType.java:163) | |
| com.sun.org.apache.xerces.internal.impl.dtd.DTDGrammar.getAttributeDecl(DTDGrammar.java:1360) | |
| com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.addDTDDefaultAttrsAndValidate(XMLDTDValidator.java:1174) | |
| TRACE 301286: | |
| java.lang.String.indexOf(String.java:1533) | |
| java.net.URLStreamHandler.parseURL(URLStreamHandler.java:144) | |
| sun.net.www.protocol.file.Handler.parseURL(Handler.java:67) | |
| TRACE 301287: | |
| java.util.Vector.<init>(Vector.java:131) | |
| java.util.Vector.<init>(Vector.java:144) | |
| java.util.Vector.<init>(Vector.java:153) | |
| TRACE 301288: | |
| com.sun.org.apache.xerces.internal.util.SymbolTable$Entry.<init>(SymbolTable.java:312) | |
| com.sun.org.apache.xerces.internal.util.SymbolTable.addSymbol(SymbolTable.java:154) | |
| com.sun.org.apache.xerces.internal.impl.XMLEntityScanner.scanName(XMLEntityScanner.java:703) | |
| TRACE 301307: | |
| com.sun.xml.internal.bind.DatatypeConverterImpl.<clinit>(DatatypeConverterImpl.java:386) | |
| com.sun.xml.internal.bind.v2.runtime.JAXBContextImpl$3.run(JAXBContextImpl.java:262) | |
| com.sun.xml.internal.bind.v2.runtime.JAXBContextImpl$3.run(JAXBContextImpl.java:260) | |
| TRACE 301391: | |
| com.sun.xml.internal.bind.v2.model.impl.RuntimeModelBuilder.createClassInfo(RuntimeModelBuilder.java:99) | |
| com.sun.xml.internal.bind.v2.model.impl.RuntimeModelBuilder.createClassInfo(RuntimeModelBuilder.java:70) | |
| com.sun.xml.internal.bind.v2.model.impl.ModelBuilder.getClassInfo(ModelBuilder.java:228) | |
| TRACE 301442: | |
| java.io.ByteArrayOutputStream.size(ByteArrayOutputStream.java:161) | |
| sun.misc.ProxyGenerator$ProxyMethod.generateMethod(ProxyGenerator.java:958) | |
| sun.misc.ProxyGenerator$ProxyMethod.access$200(ProxyGenerator.java:848) | |
| TRACE 301530: | |
| com.sun.xml.internal.bind.v2.runtime.unmarshaller.UnmarshallerImpl.unmarshal0(UnmarshallerImpl.java:300) | |
| com.sun.xml.internal.bind.v2.runtime.unmarshaller.UnmarshallerImpl.unmarshal(UnmarshallerImpl.java:286) | |
| org.broad.igv.cli_plugin.PluginSpecReader.unmarshal(PluginSpecReader.java:300) | |
| TRACE 301545: | |
| java.awt.Component.repaint(Component.java:3074) | |
| javax.swing.JComponent.setBorder(JComponent.java:1772) | |
| javax.swing.LookAndFeel.installBorder(LookAndFeel.java:227) | |
| TRACE 301549: | |
| sun.awt.X11.XWindowPeer.<init>(XWindowPeer.java:107) | |
| sun.awt.X11.XDecoratedPeer.<init>(XDecoratedPeer.java:59) | |
| sun.awt.X11.XFramePeer.<init>(XFramePeer.java:51) | |
| TRACE 301587: | |
| sun.awt.X11.XBaseWindow.getHints(XBaseWindow.java:475) | |
| sun.awt.X11.XBaseWindow.setSizeHints(XBaseWindow.java:486) | |
| sun.awt.X11.XWindow.updateSizeHints(XWindow.java:1269) | |
| TRACE 301611: | |
| sun.awt.X11.XSelection.<init>(XSelection.java:104) | |
| sun.awt.X11.XDnDConstants.<clinit>(XDnDConstants.java:51) | |
| sun.awt.X11.XDnDDropTargetProtocol.registerDropTarget(XDnDDropTargetProtocol.java:92) | |
| TRACE 301641: | |
| java.lang.Object.clone(Object.java:Unknown line) | |
| java.awt.Insets.clone(Insets.java:177) | |
| java.awt.Container.insets(Container.java:349) | |
| TRACE 301642: | |
| java.awt.EventQueue.coalesceEvent(EventQueue.java:388) | |
| java.awt.EventQueue.postEvent(EventQueue.java:257) | |
| java.awt.EventQueue.postEventPrivate(EventQueue.java:215) | |
| TRACE 301655: | |
| sun.awt.X11.XlibWrapper.XFlush(XlibWrapper.java:Unknown line) | |
| sun.awt.X11.XComponentPeer.pSetCursor(XComponentPeer.java:864) | |
| sun.awt.X11.XComponentPeer.postInit(XComponentPeer.java:150) | |
| TRACE 301683: | |
| sun.awt.X11.XlibWrapper.XWindowEvent(XlibWrapper.java:Unknown line) | |
| sun.awt.X11.XToolkit.getCurrentServerTime(XToolkit.java:1359) | |
| sun.awt.X11.XToolkit.nowMillisUTC_offset(XToolkit.java:1855) | |
| TRACE 301750: | |
| java.net.AbstractPlainSocketImpl.getOutputStream(AbstractPlainSocketImpl.java:411) | |
| java.net.Socket$3.run(Socket.java:857) | |
| java.security.AccessController.doPrivileged(AccessController.java:Unknown line) | |
| TRACE 301765: | |
| java.io.BufferedReader.readLine(BufferedReader.java:305) | |
| java.io.BufferedReader.readLine(BufferedReader.java:379) | |
| org.broad.igv.feature.genome.GenomeManager.getServerGenomeArchiveList(GenomeManager.java:715) | |
| TRACE 301768: | |
| sun.awt.X11.XlibWrapper.XQueryTree(XlibWrapper.java:Unknown line) | |
| sun.awt.X11.XQueryTree.execute(XQueryTree.java:68) | |
| sun.awt.X11.XQueryTree.execute(XQueryTree.java:52) | |
| TRACE 301771: | |
| java.lang.System.nanoTime(System.java:Unknown line) | |
| java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2095) | |
| java.util.concurrent.DelayQueue.take(DelayQueue.java:193) | |
| TRACE 301778: | |
| com.google.common.util.concurrent.ExecutionList.<init>(ExecutionList.java:52) | |
| com.google.common.util.concurrent.AbstractFuture.<init>(AbstractFuture.java:71) | |
| com.google.common.util.concurrent.SettableFuture.<init>(SettableFuture.java:41) | |
| TRACE 301783: | |
| java.security.AccessController.getStackAccessControlContext(AccessController.java:Unknown line) | |
| java.security.AccessController.getContext(AccessController.java:491) | |
| java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:116) | |
| TRACE 301799: | |
| sun.awt.X11.XlibWrapper.XSync(XlibWrapper.java:Unknown line) | |
| sun.awt.X11.XToolkit.XSync(XToolkit.java:1174) | |
| sun.awt.X11.XWM.setLayer(XWM.java:1199) | |
| TRACE 301803: | |
| sun.java2d.loops.MaskBlit.MaskBlit(MaskBlit.java:Unknown line) | |
| sun.java2d.loops.Blit$GeneralMaskBlit.Blit(Blit.java:204) | |
| sun.java2d.pipe.AlphaPaintPipe.renderPathTile(AlphaPaintPipe.java:156) | |
| TRACE 301807: | |
| java.util.HashMap.putForCreate(HashMap.java:430) | |
| java.util.HashMap.putAllForCreate(HashMap.java:453) | |
| java.util.HashMap.<init>(HashMap.java:242) | |
| TRACE 301809: | |
| sun.security.util.ManifestDigester.<init>(ManifestDigester.java:125) | |
| java.util.jar.JarVerifier.processEntry(JarVerifier.java:267) | |
| java.util.jar.JarVerifier.update(JarVerifier.java:205) | |
| TRACE 301810: | |
| sun.security.util.ManifestDigester.<init>(ManifestDigester.java:152) | |
| java.util.jar.JarVerifier.processEntry(JarVerifier.java:267) | |
| java.util.jar.JarVerifier.update(JarVerifier.java:205) | |
| TRACE 301811: | |
| java.math.BigInteger.primitiveLeftShift(BigInteger.java:1490) | |
| java.math.BigInteger.squareToLen(BigInteger.java:1318) | |
| java.math.BigInteger.oddModPow(BigInteger.java:1841) | |
| TRACE 301812: | |
| java.util.Hashtable.get(Hashtable.java:351) | |
| sun.security.util.SignatureFileVerifier.updateSigners(SignatureFileVerifier.java:636) | |
| sun.security.util.SignatureFileVerifier.processImpl(SignatureFileVerifier.java:258) | |
| TRACE 301813: | |
| java.util.HashMap.<init>(HashMap.java:200) | |
| java.util.HashMap.<init>(HashMap.java:240) | |
| java.util.jar.Attributes.<init>(Attributes.java:84) | |
| TRACE 301814: | |
| java.math.BigInteger.subN(BigInteger.java:1912) | |
| java.math.BigInteger.montReduce(BigInteger.java:1881) | |
| java.math.BigInteger.oddModPow(BigInteger.java:1747) | |
| TRACE 301820: | |
| sun.java2d.loops.GraphicsPrimitive.makeUniqueID(GraphicsPrimitive.java:131) | |
| sun.java2d.loops.GraphicsPrimitiveMgr.locatePrim(GraphicsPrimitiveMgr.java:201) | |
| sun.java2d.loops.MaskFill.locatePrim(MaskFill.java:75) | |
| TRACE 301821: | |
| java.awt.Container.mixOnValidating(Container.java:4138) | |
| java.awt.Component.validate(Component.java:2737) | |
| java.awt.Container.validateTree(Container.java:1528) | |
| TRACE 301822: | |
| java.lang.Throwable.fillInStackTrace(Throwable.java:Unknown line) | |
| java.lang.Throwable.<init>(Throwable.java:235) | |
| java.lang.Exception.<init>(Exception.java:76) | |
| TRACE 301823: | |
| net.sf.samtools.SAMFileHeader.<init>(SAMFileHeader.java:105) | |
| net.sf.samtools.SAMTextHeaderCodec.decode(SAMTextHeaderCodec.java:77) | |
| net.sf.samtools.BAMFileReader.readHeader(BAMFileReader.java:428) | |
| TRACE 301825: | |
| java.util.Hashtable.get(Hashtable.java:353) | |
| sun.security.util.SignatureFileVerifier.updateSigners(SignatureFileVerifier.java:636) | |
| sun.security.util.SignatureFileVerifier.processImpl(SignatureFileVerifier.java:258) | |
| TRACE 301828: | |
| java.security.AccessController.getStackAccessControlContext(AccessController.java:Unknown line) | |
| java.security.AccessController.getContext(AccessController.java:491) | |
| java.awt.AWTEvent.<init>(AWTEvent.java:109) | |
| TRACE 301829: | |
| javax.swing.text.GapContent.insertString(GapContent.java:133) | |
| javax.swing.text.AbstractDocument.handleInsertString(AbstractDocument.java:726) | |
| javax.swing.text.AbstractDocument.insertString(AbstractDocument.java:710) | |
| TRACE 301839: | |
| java.awt.Component.enable(Component.java:1382) | |
| javax.swing.JComponent.enable(JComponent.java:3565) | |
| java.awt.Component.enable(Component.java:1398) | |
| TRACE 301840: | |
| java.text.DontCareFieldPosition.getFieldDelegate(DontCareFieldPosition.java:51) | |
| java.text.DecimalFormat.format(DecimalFormat.java:625) | |
| java.text.NumberFormat.format(NumberFormat.java:297) | |
| TRACE 301841: | |
| javax.swing.plaf.basic.BasicComboBoxRenderer.getPreferredSize(BasicComboBoxRenderer.java:78) | |
| javax.swing.plaf.basic.BasicListUI.updateLayoutState(BasicListUI.java:1362) | |
| javax.swing.plaf.basic.BasicListUI.maybeUpdateLayoutState(BasicListUI.java:1310) | |
| TRACE 301848: | |
| java.io.StreamTokenizer.nextToken(StreamTokenizer.java:626) | |
| sun.awt.X11GraphicsEnvironment.registerFontDir(X11GraphicsEnvironment.java:803) | |
| sun.awt.X11GraphicsEnvironment.registerFontDirs(X11GraphicsEnvironment.java:761) | |
| TRACE 301854: | |
| java.nio.ByteBufferAsShortBufferB.ix(ByteBufferAsShortBufferB.java:107) | |
| java.nio.ByteBufferAsShortBufferB.get(ByteBufferAsShortBufferB.java:111) | |
| sun.font.TrueTypeFont.initNames(TrueTypeFont.java:1065) | |
| TRACE 301857: | |
| java.nio.ByteBufferAsShortBufferB.ix(ByteBufferAsShortBufferB.java:107) | |
| java.nio.ByteBufferAsShortBufferB.get(ByteBufferAsShortBufferB.java:111) | |
| sun.font.TrueTypeFont.initAllNames(TrueTypeFont.java:1253) | |
| TRACE 301858: | |
| org.broad.igv.sam.BaseAlignmentCounts.<init>(BaseAlignmentCounts.java:59) | |
| org.broad.igv.sam.DenseAlignmentCounts.<init>(DenseAlignmentCounts.java:49) | |
| org.broad.igv.sam.AlignmentTileLoader$AlignmentTile.<init>(AlignmentTileLoader.java:305) | |
| TRACE 301859: | |
| net.sf.samtools.util.BlockCompressedInputStream.getFilePointer(BlockCompressedInputStream.java:302) | |
| net.sf.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:559) | |
| net.sf.samtools.BAMFileReader$BAMFileIndexIterator.getNextRecord(BAMFileReader.java:665) | |
| TRACE 301860: | |
| net.sf.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:371) | |
| net.sf.samtools.util.BinaryCodec.readByteBuffer(BinaryCodec.java:480) | |
| net.sf.samtools.util.BinaryCodec.readUShort(BinaryCodec.java:560) | |
| TRACE 301862: | |
| java.util.ArrayList.<init>(ArrayList.java:132) | |
| java.util.ArrayList.<init>(ArrayList.java:139) | |
| net.sf.samtools.Cigar.<init>(Cigar.java:40) | |
| TRACE 301866: | |
| net.sf.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:184) | |
| net.sf.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:558) | |
| net.sf.samtools.BAMFileReader$BAMFileIndexIterator.getNextRecord(BAMFileReader.java:665) | |
| TRACE 301867: | |
| net.sf.samtools.BAMFileReader$BAMQueryFilteringIterator.advance(BAMFileReader.java:752) | |
| net.sf.samtools.BAMFileReader$BAMQueryFilteringIterator.<init>(BAMFileReader.java:701) | |
| net.sf.samtools.BAMFileReader.createIndexIterator(BAMFileReader.java:602) | |
| TRACE 301868: | |
| java.lang.Integer.intValue(Integer.java:660) | |
| net.sf.samtools.BAMFileReader$BAMQueryFilteringIterator.advance(BAMFileReader.java:752) | |
| net.sf.samtools.BAMFileReader$BAMQueryFilteringIterator.<init>(BAMFileReader.java:701) | |
| TRACE 301869: | |
| net.sf.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:193) | |
| net.sf.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:558) | |
| net.sf.samtools.BAMFileReader$BAMFileIndexIterator.getNextRecord(BAMFileReader.java:665) | |
| TRACE 301872: | |
| java.lang.Object.hashCode(Object.java:Unknown line) | |
| java.lang.Enum.hashCode(Enum.java:139) | |
| java.util.HashMap.get(HashMap.java:317) | |
| TRACE 301874: | |
| net.sf.samtools.util.StringUtil.bytesToString(StringUtil.java:301) | |
| net.sf.samtools.util.StringUtil.bytesToString(StringUtil.java:288) | |
| net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:205) | |
| TRACE 301876: | |
| java.lang.System.arraycopy(System.java:Unknown line) | |
| org.broad.igv.feature.genome.SequenceWrapper.getSequence(SequenceWrapper.java:118) | |
| org.broad.igv.feature.genome.Genome.getSequence(Genome.java:408) | |
| TRACE 301878: | |
| org.broad.igv.sam.SamAlignment.createAlignmentBlocks(SamAlignment.java:385) | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:183) | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:43) | |
| TRACE 301879: | |
| net.sf.samtools.BAMRecord.decodeReadName(BAMRecord.java:331) | |
| net.sf.samtools.BAMRecord.getReadName(BAMRecord.java:220) | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:151) | |
| TRACE 301881: | |
| net.sf.samtools.CigarElement.getLength(CigarElement.java:40) | |
| net.sf.samtools.TextCigarCodec.encode(TextCigarCodec.java:60) | |
| net.sf.samtools.SAMRecord.getCigarString(SAMRecord.java:580) | |
| TRACE 301882: | |
| org.broad.igv.sam.BisulfiteCounts.incrementCounts(BisulfiteCounts.java:70) | |
| org.broad.igv.sam.BaseAlignmentCounts.incCounts(BaseAlignmentCounts.java:91) | |
| org.broad.igv.sam.AlignmentTileLoader$AlignmentTile.addRecord(AlignmentTileLoader.java:337) | |
| TRACE 301883: | |
| net.sf.samtools.BAMFileReader$BAMQueryFilteringIterator.next(BAMFileReader.java:717) | |
| net.sf.samtools.BAMFileReader$BAMQueryFilteringIterator.next(BAMFileReader.java:673) | |
| net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:672) | |
| TRACE 301885: | |
| org.broad.igv.sam.ReadMate.<init>(ReadMate.java:40) | |
| org.broad.igv.sam.SamAlignment.setMatePair(SamAlignment.java:207) | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:164) | |
| TRACE 301886: | |
| net.sf.samtools.SAMRecord.getMappingQuality(SAMRecord.java:571) | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:150) | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:43) | |
| TRACE 301887: | |
| org.broad.igv.sam.SamAlignment.getFlowSignalsStart(SamAlignment.java:861) | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:183) | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:43) | |
| TRACE 301888: | |
| org.broad.igv.sam.PEStats.update(PEStats.java:65) | |
| org.broad.igv.sam.AlignmentTileLoader.loadTile(AlignmentTileLoader.java:190) | |
| org.broad.igv.sam.AlignmentDataManager.loadInterval(AlignmentDataManager.java:364) | |
| TRACE 301889: | |
| org.broad.igv.sam.AlignmentTileLoader.loadTile(AlignmentTileLoader.java:122) | |
| org.broad.igv.sam.AlignmentDataManager.loadInterval(AlignmentDataManager.java:364) | |
| org.broad.igv.sam.AlignmentDataManager$2.run(AlignmentDataManager.java:334) | |
| TRACE 301890: | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:183) | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:43) | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:26) | |
| TRACE 301892: | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:81) | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:43) | |
| org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:26) | |
| TRACE 301894: | |
| javax.swing.JComponent.getFlag(JComponent.java:5226) | |
| javax.swing.JComponent.isDoubleBuffered(JComponent.java:5262) | |
| javax.swing.JComponent._paintImmediately(JComponent.java:5032) | |
| TRACE 301897: | |
| org.broad.igv.sam.AlignmentTrack.getBisulfiteContextPostContext(AlignmentTrack.java:885) | |
| org.broad.igv.sam.BisulfiteCounts.contextIsMatching(BisulfiteCounts.java:144) | |
| org.broad.igv.sam.BisulfiteCounts.incrementCounts(BisulfiteCounts.java:83) | |
| TRACE 301900: | |
| java.lang.Thread.currentThread(Thread.java:Unknown line) | |
| java.util.concurrent.locks.ReentrantLock$Sync.tryRelease(ReentrantLock.java:154) | |
| java.util.concurrent.locks.AbstractQueuedSynchronizer.release(AbstractQueuedSynchronizer.java:1262) | |
| TRACE 301907: | |
| net.sf.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:75) | |
| net.sf.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:383) | |
| net.sf.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:365) | |
| TRACE 301910: | |
| org.broad.igv.sam.AlignmentBlock.getStart(AlignmentBlock.java:71) | |
| org.broad.igv.sam.DenseAlignmentCounts.incrementInsertion(DenseAlignmentCounts.java:301) | |
| org.broad.igv.sam.BaseAlignmentCounts.incCounts(BaseAlignmentCounts.java:137) | |
| TRACE 301913: | |
| javax.swing.JComponent.setFlag(JComponent.java:5220) | |
| javax.swing.JComponent.paintChildren(JComponent.java:856) | |
| javax.swing.JComponent.paint(JComponent.java:1038) | |
| TRACE 301914: | |
| java.util.LinkedHashMap.addEntry(LinkedHashMap.java:423) | |
| java.util.HashMap.put(HashMap.java:402) | |
| org.broad.igv.util.ObjectCache.put(ObjectCache.java:66) | |
| TRACE 301917: | |
| java.lang.Integer.getChars(Integer.java:370) | |
| java.lang.Integer.toString(Integer.java:330) | |
| java.lang.Integer.toString(Integer.java:134) | |
| TRACE 301919: | |
| java.awt.geom.Path2D$Float.append(Path2D.java:655) | |
| java.awt.geom.Path2D.append(Path2D.java:1797) | |
| javax.swing.border.LineBorder.paintBorder(LineBorder.java:143) | |
| TRACE 301920: | |
| org.broad.igv.sam.AlignmentTileLoader$AlignmentTile.addRecord(AlignmentTileLoader.java:340) | |
| org.broad.igv.sam.AlignmentTileLoader.loadTile(AlignmentTileLoader.java:168) | |
| org.broad.igv.sam.AlignmentDataManager.loadInterval(AlignmentDataManager.java:364) | |
| TRACE 301924: | |
| java.util.TaskQueue.getMin(Timer.java:589) | |
| java.util.TimerThread.mainLoop(Timer.java:511) | |
| java.util.TimerThread.run(Timer.java:484) | |
| TRACE 301926: | |
| net.sf.samtools.SAMBinaryTagAndValue.find(SAMBinaryTagAndValue.java:119) | |
| net.sf.samtools.SAMBinaryTagAndValue.find(SAMBinaryTagAndValue.java:119) | |
| net.sf.samtools.SAMBinaryTagAndValue.find(SAMBinaryTagAndValue.java:119) | |
| TRACE 301928: | |
| net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:339) | |
| net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:269) | |
| net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:201) | |
| TRACE 301929: | |
| java.lang.StringBuffer.toString(StringBuffer.java:602) | |
| org.broad.igv.sam.SamAlignment.createAlignmentBlocks(SamAlignment.java:360) | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:183) | |
| TRACE 301931: | |
| java.awt.Component.getGraphicsConfiguration(Component.java:1029) | |
| javax.swing.RepaintManager.getVolatileOffscreenBuffer(RepaintManager.java:963) | |
| javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1370) | |
| TRACE 301933: | |
| org.apache.commons.math.stat.descriptive.moment.Variance.<init>(Variance.java:95) | |
| org.apache.commons.math.stat.StatUtils.<clinit>(StatUtils.java:64) | |
| org.broad.igv.sam.PEStats.computePercentile(PEStats.java:137) | |
| TRACE 301934: | |
| org.apache.commons.math.util.FastMath.quadMult(FastMath.java:1130) | |
| org.apache.commons.math.util.FastMath.expint(FastMath.java:1207) | |
| org.apache.commons.math.util.FastMath.<clinit>(FastMath.java:218) | |
| TRACE 301935: | |
| org.apache.commons.math.util.FastMath.slowexp(FastMath.java:999) | |
| org.apache.commons.math.util.FastMath.<clinit>(FastMath.java:232) | |
| org.apache.commons.math.stat.descriptive.rank.Percentile.evaluate(Percentile.java:272) | |
| TRACE 301936: | |
| org.apache.commons.math.util.FastMath.slowLog(FastMath.java:1747) | |
| org.apache.commons.math.util.FastMath.<clinit>(FastMath.java:240) | |
| org.apache.commons.math.stat.descriptive.rank.Percentile.evaluate(Percentile.java:272) | |
| TRACE 301937: | |
| java.awt.Component.getGraphicsConfiguration(Component.java:1029) | |
| javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1374) | |
| javax.swing.BufferStrategyPaintManager.paint(BufferStrategyPaintManager.java:318) | |
| TRACE 301938: | |
| java.util.Arrays.mergeSort(Arrays.java:1278) | |
| java.util.Arrays.mergeSort(Arrays.java:1295) | |
| java.util.Arrays.mergeSort(Arrays.java:1295) | |
| TRACE 301939: | |
| java.util.Arrays.mergeSort(Arrays.java:1278) | |
| java.util.Arrays.mergeSort(Arrays.java:1295) | |
| java.util.Arrays.mergeSort(Arrays.java:1294) | |
| TRACE 301940: | |
| java.util.ArrayList.set(ArrayList.java:367) | |
| java.util.ArrayList$ListItr.set(ArrayList.java:826) | |
| java.util.Collections.sort(Collections.java:180) | |
| TRACE 301941: | |
| java.util.Arrays.copyOf(Arrays.java:2772) | |
| java.util.Arrays.copyOf(Arrays.java:2746) | |
| java.util.PriorityQueue.grow(PriorityQueue.java:255) | |
| TRACE 301942: | |
| org.broad.igv.sam.AlignmentPacker.pack(AlignmentPacker.java:277) | |
| org.broad.igv.sam.AlignmentPacker.packAlignments(AlignmentPacker.java:68) | |
| org.broad.igv.sam.AlignmentDataManager.loadInterval(AlignmentDataManager.java:384) | |
| TRACE 301952: | |
| sun.misc.Unsafe.compareAndSwapInt(Unsafe.java:Unknown line) | |
| java.util.concurrent.locks.AbstractQueuedSynchronizer.compareAndSetState(AbstractQueuedSynchronizer.java:570) | |
| java.util.concurrent.locks.ReentrantLock$NonfairSync.lock(ReentrantLock.java:211) | |
| TRACE 301954: | |
| sun.java2d.pipe.PixelToParallelogramConverter.fillRectangle(PixelToParallelogramConverter.java:309) | |
| sun.java2d.pipe.PixelToParallelogramConverter.fillRect(PixelToParallelogramConverter.java:115) | |
| sun.java2d.SunGraphics2D.fillRect(SunGraphics2D.java:2319) | |
| TRACE 301955: | |
| org.broad.igv.sam.CoverageTrack.drawBar(CoverageTrack.java:500) | |
| org.broad.igv.sam.CoverageTrack$IntervalRenderer.paint(CoverageTrack.java:453) | |
| org.broad.igv.sam.CoverageTrack$IntervalRenderer.access$000(CoverageTrack.java:313) | |
| TRACE 301966: | |
| java.text.NumberFormat.getMinimumIntegerDigits(NumberFormat.java:593) | |
| java.text.DecimalFormat.format(DecimalFormat.java:684) | |
| java.text.DecimalFormat.format(DecimalFormat.java:625) | |
| TRACE 301970: | |
| org.broad.igv.sam.AlignmentRenderer.drawBase(AlignmentRenderer.java:924) | |
| org.broad.igv.sam.AlignmentRenderer.drawBases(AlignmentRenderer.java:780) | |
| org.broad.igv.sam.AlignmentRenderer.drawAlignment(AlignmentRenderer.java:616) | |
| TRACE 301971: | |
| sun.java2d.x11.X11Renderer.XFillRect(X11Renderer.java:Unknown line) | |
| sun.java2d.x11.X11Renderer.fillRect(X11Renderer.java:211) | |
| sun.java2d.pipe.ValidatePipe.fillRect(ValidatePipe.java:76) | |
| TRACE 301972: | |
| java.lang.Thread.currentThread(Thread.java:Unknown line) | |
| java.util.concurrent.locks.AbstractQueuedSynchronizer.addWaiter(AbstractQueuedSynchronizer.java:610) | |
| java.util.concurrent.locks.AbstractQueuedSynchronizer.acquire(AbstractQueuedSynchronizer.java:1201) | |
| TRACE 301973: | |
| org.broad.igv.sam.AlignmentRenderer.drawBase(AlignmentRenderer.java:928) | |
| org.broad.igv.sam.AlignmentRenderer.drawBases(AlignmentRenderer.java:780) | |
| org.broad.igv.sam.AlignmentRenderer.drawAlignment(AlignmentRenderer.java:616) | |
| TRACE 301977: | |
| sun.java2d.x11.X11SurfaceData.validatePipe(X11SurfaceData.java:346) | |
| sun.java2d.SunGraphics2D.validatePipe(SunGraphics2D.java:383) | |
| sun.java2d.pipe.ValidatePipe.validate(ValidatePipe.java:55) | |
| TRACE 301978: | |
| org.broad.igv.sam.AlignmentRenderer.renderAlignments(AlignmentRenderer.java:288) | |
| org.broad.igv.sam.AlignmentTrack.renderAlignments(AlignmentTrack.java:412) | |
| org.broad.igv.sam.AlignmentTrack.render(AlignmentTrack.java:324) | |
| TRACE 301980: | |
| org.broad.igv.sam.AlignmentBlock.getStart(AlignmentBlock.java:71) | |
| org.broad.igv.sam.AlignmentRenderer.drawAlignment(AlignmentRenderer.java:524) | |
| org.broad.igv.sam.AlignmentRenderer.renderAlignments(AlignmentRenderer.java:288) | |
| TRACE 301981: | |
| java.lang.Integer.hashCode(Integer.java:709) | |
| java.util.WeakHashMap.get(WeakHashMap.java:373) | |
| org.broad.igv.ui.color.ColorUtilities.getCompositeColor(ColorUtilities.java:251) | |
| TRACE 301982: | |
| java.lang.Thread.currentThread(Thread.java:Unknown line) | |
| java.util.concurrent.locks.LockSupport.park(LockSupport.java:184) | |
| java.util.concurrent.locks.AbstractQueuedSynchronizer.parkAndCheckInterrupt(AbstractQueuedSynchronizer.java:838) | |
| TRACE 301983: | |
| java.lang.StrictMath.ceil(StrictMath.java:Unknown line) | |
| java.lang.Math.ceil(Math.java:405) | |
| sun.java2d.pisces.Renderer$ScanlineIterator.<init>(Renderer.java:76) | |
| TRACE 301984: | |
| java.util.Hashtable.containsKey(Hashtable.java:323) | |
| org.broad.igv.IGVPreferences.get(IGVPreferences.java:85) | |
| org.broad.igv.PreferenceManager.get(PreferenceManager.java:267) | |
| TRACE 301985: | |
| java.lang.System.arraycopy(System.java:Unknown line) | |
| java.text.DigitList.set(DigitList.java:543) | |
| java.text.DecimalFormat.format(DecimalFormat.java:688) | |
| TRACE 301989: | |
| sun.java2d.x11.X11Renderer.XDoPath(X11Renderer.java:Unknown line) | |
| sun.java2d.x11.X11Renderer.doPath(X11Renderer.java:318) | |
| sun.java2d.x11.X11Renderer.fill(X11Renderer.java:375) | |
| TRACE 301993: | |
| java.util.regex.Matcher.<init>(Matcher.java:224) | |
| java.util.regex.Pattern.matcher(Pattern.java:905) | |
| java.lang.String.replace(String.java:2219) | |
| TRACE 301994: | |
| sun.java2d.pisces.PiscesCache.addTupleToRow(PiscesCache.java:164) | |
| sun.java2d.pisces.PiscesCache.addRLERun(PiscesCache.java:83) | |
| sun.java2d.pisces.Renderer.emitRow(Renderer.java:860) | |
| TRACE 301998: | |
| sun.security.util.SignatureFileVerifier.updateSigners(SignatureFileVerifier.java:636) | |
| sun.security.util.SignatureFileVerifier.processImpl(SignatureFileVerifier.java:258) | |
| sun.security.util.SignatureFileVerifier.process(SignatureFileVerifier.java:193) | |
| TRACE 301999: | |
| java.lang.String.lastIndexOf(String.java:1639) | |
| java.net.URLClassLoader.defineClass(URLClassLoader.java:232) | |
| java.net.URLClassLoader.access$000(URLClassLoader.java:73) | |
| TRACE 302000: | |
| com.google.gson.stream.StringPool.get(StringPool.java:35) | |
| com.google.gson.stream.JsonReader.nextString(JsonReader.java:1021) | |
| com.google.gson.stream.JsonReader.nextValue(JsonReader.java:784) | |
| TRACE 302001: | |
| java.util.HashMap.put(HashMap.java:389) | |
| sun.security.util.ManifestDigester.<init>(ManifestDigester.java:168) | |
| java.util.jar.JarVerifier.processEntry(JarVerifier.java:267) | |
| TRACE 302002: | |
| net.sf.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:189) | |
| net.sf.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:558) | |
| net.sf.samtools.BAMFileReader$BAMFileIndexIterator.getNextRecord(BAMFileReader.java:665) | |
| TRACE 302003: | |
| java.util.ArrayList.iterator(ArrayList.java:737) | |
| net.sf.samtools.Cigar.getReferenceLength(Cigar.java:74) | |
| net.sf.samtools.SAMRecord.getAlignmentEnd(SAMRecord.java:456) | |
| TRACE 302004: | |
| net.sf.samtools.util.BinaryCodec.readUByte(BinaryCodec.java:549) | |
| net.sf.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:191) | |
| net.sf.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:558) | |
| TRACE 302005: | |
| net.sf.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:192) | |
| net.sf.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:558) | |
| net.sf.samtools.BAMFileReader$BAMFileIndexIterator.getNextRecord(BAMFileReader.java:665) | |
| TRACE 302006: | |
| org.broad.igv.sam.AbstractAlignment.getReadName(AbstractAlignment.java:65) | |
| org.broad.igv.sam.AlignmentTileLoader.loadTile(AlignmentTileLoader.java:130) | |
| org.broad.igv.sam.AlignmentDataManager.loadInterval(AlignmentDataManager.java:364) | |
| TRACE 302007: | |
| org.broad.igv.sam.AlignmentTileLoader.loadTile(AlignmentTileLoader.java:126) | |
| org.broad.igv.sam.AlignmentDataManager.loadInterval(AlignmentDataManager.java:364) | |
| org.broad.igv.sam.AlignmentDataManager$2.run(AlignmentDataManager.java:334) | |
| TRACE 302008: | |
| org.broad.igv.sam.AlignmentTileLoader.loadTile(AlignmentTileLoader.java:171) | |
| org.broad.igv.sam.AlignmentDataManager.loadInterval(AlignmentDataManager.java:364) | |
| org.broad.igv.sam.AlignmentDataManager$2.run(AlignmentDataManager.java:334) | |
| TRACE 302009: | |
| javax.swing.JComponent.paint(JComponent.java:1004) | |
| javax.swing.JComponent.paintChildren(JComponent.java:866) | |
| javax.swing.JComponent.paint(JComponent.java:1038) | |
| TRACE 302013: | |
| javax.swing.JComponent.paintChildren(JComponent.java:799) | |
| javax.swing.JComponent.paint(JComponent.java:1038) | |
| javax.swing.JLayeredPane.paint(JLayeredPane.java:581) | |
| TRACE 302014: | |
| org.broad.igv.sam.AlignmentTileLoader$AlignmentTile.emptyBucket(AlignmentTileLoader.java:366) | |
| org.broad.igv.sam.AlignmentTileLoader$AlignmentTile.addRecord(AlignmentTileLoader.java:347) | |
| org.broad.igv.sam.AlignmentTileLoader.loadTile(AlignmentTileLoader.java:168) | |
| TRACE 302016: | |
| java.util.HashMap.size(HashMap.java:285) | |
| org.broad.igv.util.ObjectCache.put(ObjectCache.java:57) | |
| org.broad.igv.sam.AlignmentTileLoader.loadTile(AlignmentTileLoader.java:150) | |
| TRACE 302019: | |
| java.lang.Object.hashCode(Object.java:Unknown line) | |
| java.util.concurrent.ConcurrentHashMap.get(ConcurrentHashMap.java:796) | |
| sun.awt.image.SurfaceManager.getCacheData(SurfaceManager.java:114) | |
| TRACE 302021: | |
| net.sf.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:342) | |
| net.sf.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:113) | |
| net.sf.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:238) | |
| TRACE 302023: | |
| sun.font.FontManager.getFont2D(FontManager.java:Unknown line) | |
| sun.java2d.SunGraphics2D.checkFontInfo(SunGraphics2D.java:606) | |
| sun.java2d.SunGraphics2D.getFontInfo(SunGraphics2D.java:766) | |
| TRACE 302025: | |
| java.util.Arrays.mergeSort(Arrays.java:1283) | |
| java.util.Arrays.mergeSort(Arrays.java:1295) | |
| java.util.Arrays.mergeSort(Arrays.java:1295) | |
| TRACE 302026: | |
| sun.java2d.pipe.AlphaColorPipe.renderPathTile(AlphaColorPipe.java:55) | |
| sun.java2d.pipe.AAShapePipe.renderTiles(AAShapePipe.java:201) | |
| sun.java2d.pipe.AAShapePipe.renderPath(AAShapePipe.java:159) | |
| TRACE 302031: | |
| java.lang.String.toCharArray(String.java:2737) | |
| java.awt.Font.getStringBounds(Font.java:2240) | |
| java.awt.FontMetrics.getStringBounds(FontMetrics.java:531) | |
| TRACE 302032: | |
| sun.misc.Unsafe.getFloat(Unsafe.java:Unknown line) | |
| sun.font.FileFontStrike.getGlyphMetrics(FileFontStrike.java:642) | |
| sun.font.CompositeStrike.getGlyphMetrics(CompositeStrike.java:138) | |
| TRACE 302033: | |
| java.lang.Integer.hashCode(Integer.java:709) | |
| java.util.concurrent.ConcurrentHashMap.get(ConcurrentHashMap.java:796) | |
| sun.java2d.pisces.PiscesTileGenerator.getAlphaMap(PiscesTileGenerator.java:75) | |
| TRACE 302034: | |
| org.broad.igv.PreferenceManager.getAsInt(PreferenceManager.java:313) | |
| org.broad.igv.sam.AlignmentRenderer.getShadedColor(AlignmentRenderer.java:939) | |
| org.broad.igv.sam.AlignmentRenderer.drawBases(AlignmentRenderer.java:759) | |
| TRACE 302035: | |
| java.awt.Color.hashCode(Color.java:676) | |
| java.util.HashMap.get(HashMap.java:317) | |
| java.util.Collections$SynchronizedMap.get(Collections.java:1990) | |
| TRACE 302036: | |
| org.broad.igv.sam.AlignmentRenderer.drawAlignment(AlignmentRenderer.java:519) | |
| org.broad.igv.sam.AlignmentRenderer.renderAlignments(AlignmentRenderer.java:288) | |
| org.broad.igv.sam.AlignmentTrack.renderAlignments(AlignmentTrack.java:412) | |
| TRACE 302037: | |
| sun.java2d.pisces.Helpers.widenArray(Helpers.java:178) | |
| sun.java2d.pisces.Renderer.addPathSegment(Renderer.java:505) | |
| sun.java2d.pisces.Renderer.somethingTo(Renderer.java:569) | |
| TRACE 302038: | |
| sun.font.GlyphList.getInstance(GlyphList.java:197) | |
| sun.java2d.pipe.GlyphListPipe.drawString(GlyphListPipe.java:70) | |
| sun.java2d.pipe.ValidatePipe.drawString(ValidatePipe.java:165) | |
| TRACE 302039: | |
| org.broad.igv.sam.AlignmentTrack.renderAlignments(AlignmentTrack.java:402) | |
| org.broad.igv.sam.AlignmentTrack.render(AlignmentTrack.java:324) | |
| org.broad.igv.ui.panel.DataPanelPainter.draw(DataPanelPainter.java:260) | |
| TRACE 302040: | |
| sun.java2d.SunGraphics2D.validateBasicStroke(SunGraphics2D.java:984) | |
| sun.java2d.SunGraphics2D.setStroke(SunGraphics2D.java:1096) | |
| org.broad.igv.renderer.GraphicUtils.drawDashedLine(GraphicUtils.java:232) | |
| TRACE 302041: | |
| java.awt.Container.getComponent(Container.java:304) | |
| javax.swing.JComponent.paintChildren(JComponent.java:817) | |
| javax.swing.JComponent.paint(JComponent.java:1038) | |
| TRACE 302042: | |
| java.awt.Container.addImpl(Container.java:1075) | |
| javax.swing.CellRendererPane.addImpl(CellRendererPane.java:106) | |
| java.awt.Container.add(Container.java:373) | |
| TRACE 302043: | |
| net.sf.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:195) | |
| net.sf.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:558) | |
| net.sf.samtools.BAMFileReader$BAMFileIndexIterator.getNextRecord(BAMFileReader.java:665) | |
| TRACE 302044: | |
| net.sf.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:196) | |
| net.sf.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:558) | |
| net.sf.samtools.BAMFileReader$BAMFileIndexIterator.getNextRecord(BAMFileReader.java:665) | |
| TRACE 302045: | |
| org.broad.igv.feature.genome.SequenceWrapper.getSequenceTile(SequenceWrapper.java:141) | |
| org.broad.igv.feature.genome.SequenceWrapper.getSequence(SequenceWrapper.java:93) | |
| org.broad.igv.feature.genome.Genome.getSequence(Genome.java:408) | |
| TRACE 302046: | |
| org.broad.igv.feature.genome.SequenceWrapper.getSequenceTile(SequenceWrapper.java:141) | |
| org.broad.igv.feature.genome.SequenceWrapper.getSequence(SequenceWrapper.java:93) | |
| org.broad.igv.feature.genome.Genome.getSequence(Genome.java:408) | |
| TRACE 302047: | |
| java.util.HashMap.get(HashMap.java:317) | |
| org.broad.igv.sam.AlignmentTrack.getBisulfiteContextPostContext(AlignmentTrack.java:885) | |
| org.broad.igv.sam.BisulfiteCounts.contextIsMatching(BisulfiteCounts.java:144) | |
| TRACE 302048: | |
| javax.swing.JComponent.getInsets(JComponent.java:1817) | |
| javax.swing.plaf.basic.BasicLabelUI.layout(BasicLabelUI.java:191) | |
| javax.swing.plaf.basic.BasicLabelUI.paint(BasicLabelUI.java:165) | |
| TRACE 302049: | |
| sun.java2d.x11.XSurfaceData.XSetClip(XSurfaceData.java:Unknown line) | |
| sun.java2d.x11.X11SurfaceData.getGC(X11SurfaceData.java:621) | |
| sun.java2d.x11.X11SurfaceData.getRenderGC(X11SurfaceData.java:599) | |
| TRACE 302050: | |
| java.util.Hashtable.size(Hashtable.java:223) | |
| javax.swing.DebugGraphics.debugComponentCount(DebugGraphics.java:1413) | |
| javax.swing.JComponent.getComponentGraphics(JComponent.java:719) | |
| TRACE 302052: | |
| org.broad.igv.sam.AlignmentTileLoader$AlignmentTile.addRecord(AlignmentTileLoader.java:337) | |
| org.broad.igv.sam.AlignmentTileLoader.loadTile(AlignmentTileLoader.java:168) | |
| org.broad.igv.sam.AlignmentDataManager.loadInterval(AlignmentDataManager.java:364) | |
| TRACE 302053: | |
| net.sf.samtools.BinaryTagCodec.readSingleValue(BinaryTagCodec.java:318) | |
| net.sf.samtools.BinaryTagCodec.readTags(BinaryTagCodec.java:282) | |
| net.sf.samtools.BAMRecord.decodeAttributes(BAMRecord.java:308) | |
| TRACE 302054: | |
| org.broad.igv.sam.SamAlignment.getReadSequence(SamAlignment.java:593) | |
| org.broad.igv.sam.AlignmentTileLoader.loadTile(AlignmentTileLoader.java:152) | |
| org.broad.igv.sam.AlignmentDataManager.loadInterval(AlignmentDataManager.java:364) | |
| TRACE 302055: | |
| org.broad.igv.sam.AlignmentTileLoader.loadTile(AlignmentTileLoader.java:160) | |
| org.broad.igv.sam.AlignmentDataManager.loadInterval(AlignmentDataManager.java:364) | |
| org.broad.igv.sam.AlignmentDataManager$2.run(AlignmentDataManager.java:334) | |
| TRACE 302056: | |
| org.broad.igv.PreferenceManager.getAsBoolean(PreferenceManager.java:293) | |
| org.broad.igv.sam.SamAlignment.createAlignmentBlocks(SamAlignment.java:331) | |
| org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:183) | |
| TRACE 302057: | |
| org.broad.igv.sam.BaseAlignmentCounts.incCounts(BaseAlignmentCounts.java:91) | |
| org.broad.igv.sam.AlignmentTileLoader$AlignmentTile.addRecord(AlignmentTileLoader.java:337) | |
| org.broad.igv.sam.AlignmentTileLoader.loadTile(AlignmentTileLoader.java:168) | |
| TRACE 302058: | |
| org.broad.igv.sam.AlignmentTileLoader.loadTile(AlignmentTileLoader.java:190) | |
| org.broad.igv.sam.AlignmentDataManager.loadInterval(AlignmentDataManager.java:364) | |
| org.broad.igv.sam.AlignmentDataManager$2.run(AlignmentDataManager.java:334) | |
| TRACE 302059: | |
| sun.java2d.x11.X11SurfaceData.getBlitGC(X11SurfaceData.java:603) | |
| sun.java2d.x11.X11PMBlitLoops.Blit(X11PMBlitLoops.java:142) | |
| sun.java2d.pipe.DrawImage.blitSurfaceData(DrawImage.java:956) | |
| TRACE 302060: | |
| org.broad.igv.sam.AlignmentTileLoader$AlignmentTile$SamplingBucket.<init>(AlignmentTileLoader.java:424) | |
| org.broad.igv.sam.AlignmentTileLoader$AlignmentTile.addRecord(AlignmentTileLoader.java:350) | |
| org.broad.igv.sam.AlignmentTileLoader.loadTile(AlignmentTileLoader.java:168) | |
| TRACE 302061: | |
| javax.swing.RepaintManager.addDirtyRegion0(RepaintManager.java:404) | |
| javax.swing.RepaintManager.addDirtyRegion(RepaintManager.java:468) | |
| javax.swing.JComponent.repaint(JComponent.java:4736) | |
| TRACE 302062: | |
| java.lang.Object.getClass(Object.java:Unknown line) | |
| java.util.Arrays.copyOf(Arrays.java:2746) | |
| java.util.PriorityQueue.grow(PriorityQueue.java:255) | |
| TRACE 302063: | |
| org.broad.igv.sam.AbstractAlignment.getMappingQuality(AbstractAlignment.java:69) | |
| org.broad.igv.sam.AlignmentRenderer.getAlignmentColor(AlignmentRenderer.java:1099) | |
| org.broad.igv.sam.AlignmentRenderer.renderAlignments(AlignmentRenderer.java:285) | |
| TRACE 302064: | |
| java.lang.StrictMath.floor(StrictMath.java:Unknown line) | |
| java.lang.Math.floor(Math.java:424) | |
| sun.java2d.pipe.PixelToParallelogramConverter.normalize(PixelToParallelogramConverter.java:174) | |
| TRACE 302065: | |
| org.broad.igv.sam.AlignmentRenderer.drawAlignment(AlignmentRenderer.java:518) | |
| org.broad.igv.sam.AlignmentRenderer.renderAlignments(AlignmentRenderer.java:288) | |
| org.broad.igv.sam.AlignmentTrack.renderAlignments(AlignmentTrack.java:412) | |
| TRACE 302066: | |
| sun.java2d.loops.MaskBlit.MaskBlit(MaskBlit.java:Unknown line) | |
| sun.java2d.loops.Blit$GeneralMaskBlit.Blit(Blit.java:204) | |
| sun.java2d.pipe.DrawImage.blitSurfaceData(DrawImage.java:956) | |
| CPU SAMPLES BEGIN (total = 9132) Fri Jul 19 08:24:07 2013 | |
| rank self accum count trace method | |
| 1 37.25% 37.25% 3402 301784 java.net.PlainSocketImpl.socketAccept | |
| 2 23.03% 60.28% 2103 301951 sun.java2d.loops.MaskFill.FillAAPgram | |
| 3 21.24% 81.53% 1940 300768 sun.awt.X11.XToolkit.waitForEvents | |
| 4 4.91% 86.43% 448 301826 sun.java2d.loops.MaskFill.FillAAPgram | |
| 5 3.02% 89.45% 276 301956 sun.java2d.loops.MaskFill.DrawAAPgram | |
| 6 0.89% 90.34% 81 301953 sun.misc.Unsafe.unpark | |
| 7 0.65% 90.99% 59 301865 java.util.zip.Inflater.inflateBytes | |
| 8 0.62% 91.61% 57 301895 org.broad.igv.sam.DenseAlignmentCounts.incBlockCounts | |
| 9 0.46% 92.07% 42 301965 sun.awt.X11.XlibWrapper.XEventsQueued | |
| 10 0.44% 92.51% 40 301901 org.broad.igv.sam.SamAlignment.getFileSource | |
| 11 0.44% 92.95% 40 301968 sun.java2d.loops.MaskFill.MaskFill | |
| 12 0.42% 93.36% 38 301898 net.sf.samtools.SAMRecord.getFileSource | |
| 13 0.31% 93.67% 28 301896 org.broad.igv.sam.BisulfiteCounts.incrementCounts | |
| 14 0.21% 93.88% 19 300020 java.lang.String.intern | |
| 15 0.21% 94.09% 19 301891 org.broad.igv.sam.SamAlignment.getFileSource | |
| 16 0.15% 94.24% 14 301871 net.sf.samtools.util.BlockCompressedInputStream.read | |
| 17 0.15% 94.39% 14 301912 net.sf.samtools.SAMRecord.getFileSource | |
| 18 0.14% 94.54% 13 300031 java.util.zip.Inflater.inflateBytes | |
| 19 0.14% 94.68% 13 301824 sun.awt.X11.XlibWrapper.XEventsQueued | |
| 20 0.13% 94.81% 12 301911 java.nio.ByteBuffer.get | |
| 21 0.13% 94.94% 12 301969 sun.java2d.loops.MaskFill.FillAAPgram | |
| 22 0.12% 95.06% 11 301979 java.lang.StrictMath.ceil | |
| 23 0.11% 95.17% 10 301974 sun.misc.Unsafe.park | |
| 24 0.10% 95.27% 9 302030 sun.java2d.loops.DrawGlyphListAA.DrawGlyphListAA | |
| 25 0.08% 95.35% 7 301864 net.sf.samtools.util.BlockCompressedInputStream.inflateBlock | |
| 26 0.08% 95.42% 7 301906 java.util.Hashtable.get | |
| 27 0.07% 95.49% 6 300301 sun.nio.cs.UTF_8.updatePositions | |
| 28 0.07% 95.55% 6 301827 java.security.AccessController.doPrivileged | |
| 29 0.07% 95.62% 6 301930 java.util.HashMap.getEntry | |
| 30 0.07% 95.69% 6 302017 org.broad.igv.sam.AlignmentTileLoader$AlignmentTile.addRecord | |
| 31 0.05% 95.74% 5 300017 java.lang.StringCoding$StringDecoder.decode | |
| 32 0.05% 95.80% 5 300256 sun.security.provider.DigestBase.engineUpdate | |
| 33 0.05% 95.85% 5 300777 java.io.FileInputStream.readBytes | |
| 34 0.05% 95.90% 5 300778 java.lang.UNIXProcess.waitForProcessExit | |
| 35 0.05% 95.96% 5 301755 java.net.SocketInputStream.socketRead0 | |
| 36 0.05% 96.01% 5 301870 net.sf.samtools.BAMFileReader$BAMFileIterator.next | |
| 37 0.05% 96.07% 5 301905 java.util.HashMap.get | |
| 38 0.05% 96.12% 5 301925 java.io.RandomAccessFile.readBytes | |
| 39 0.05% 96.18% 5 301967 sun.java2d.x11.X11SurfaceData.XSetForeground | |
| 40 0.05% 96.23% 5 302015 java.lang.Integer.parseInt | |
| 41 0.04% 96.28% 4 301733 java.net.Inet6AddressImpl.lookupAllHostAddr | |
| 42 0.04% 96.32% 4 301808 java.util.HashMap.transfer | |
| 43 0.04% 96.36% 4 301861 net.sf.samtools.BAMRecordCodec.decode | |
| 44 0.04% 96.41% 4 301893 org.broad.igv.sam.reader.WrappedIterator.next | |
| 45 0.04% 96.45% 4 301899 java.util.Hashtable.get | |
| 46 0.04% 96.50% 4 301902 org.broad.igv.sam.SamAlignment.createAlignmentBlocks | |
| 47 0.04% 96.54% 4 301908 java.lang.Integer.toString | |
| 48 0.04% 96.58% 4 301915 org.broad.igv.sam.SamAlignment.createAlignmentBlocks | |
| 49 0.04% 96.63% 4 301918 org.broad.igv.sam.BisulfiteCounts.positionMatchesContext | |
| 50 0.04% 96.67% 4 301923 net.sf.samtools.BinaryCigarCodec.decode | |
| 51 0.04% 96.71% 4 302020 org.broad.igv.sam.SamAlignment.createAlignmentBlocks | |
| 52 0.04% 96.76% 4 302024 net.sf.samtools.BinaryTagCodec.readTags | |
| 53 0.03% 96.79% 3 300016 java.util.HashMap.<init> | |
| 54 0.03% 96.82% 3 300274 java.lang.ClassLoader.defineClass1 | |
| 55 0.03% 96.86% 3 301653 sun.awt.X11.XlibWrapper.XGetWindowAttributes | |
| 56 0.03% 96.89% 3 301654 sun.awt.X11.XlibWrapper.XSync | |
| 57 0.03% 96.92% 3 301873 org.broad.igv.sam.SamAlignment.setPairOrientation | |
| 58 0.03% 96.96% 3 301880 org.broad.igv.feature.genome.SequenceWrapper.getSequence | |
| 59 0.03% 96.99% 3 301884 net.sf.samtools.BAMRecord.decodeBaseQualities | |
| 60 0.03% 97.02% 3 301903 net.sf.samtools.SAMBinaryTagAndValue.find | |
| 61 0.03% 97.05% 3 301909 java.util.HashMap.getEntry | |
| 62 0.03% 97.09% 3 301922 net.sf.samtools.SAMReadGroupRecord.getPlatform | |
| 63 0.03% 97.12% 3 301927 java.lang.StringBuilder.append | |
| 64 0.03% 97.15% 3 302010 net.sf.samtools.util.StringUtil.bytesToString | |
| 65 0.02% 97.17% 2 300001 java.lang.ClassLoader.findBootstrapClass | |
| 66 0.02% 97.20% 2 300275 sun.security.util.ManifestEntryVerifier.update | |
| 67 0.02% 97.22% 2 300294 java.util.zip.ZipFile.getEntry | |
| 68 0.02% 97.24% 2 300576 sun.awt.X11GraphicsEnvironment.initDisplay | |
| 69 0.02% 97.26% 2 301029 java.lang.System.arraycopy | |
| 70 0.02% 97.28% 2 301676 sun.awt.X11.XlibWrapper.XGetIconSizes | |
| 71 0.02% 97.31% 2 301734 sun.awt.X11.XInputMethod.openXIMNative | |
| 72 0.02% 97.33% 2 301875 sun.misc.Unsafe.compareAndSwapLong | |
| 73 0.02% 97.35% 2 301877 java.lang.System.arraycopy | |
| 74 0.02% 97.37% 2 301904 net.sf.samtools.BAMRecord.decodeAttributes | |
| 75 0.02% 97.39% 2 301916 org.broad.igv.feature.genome.Genome.getSequence | |
| 76 0.02% 97.42% 2 301921 net.sf.samtools.BAMRecord.getCigar | |
| 77 0.02% 97.44% 2 301932 org.broad.igv.feature.genome.Genome.getChromosome | |
| 78 0.02% 97.46% 2 301976 java.lang.StrictMath.ceil | |
| 79 0.02% 97.48% 2 302011 org.broad.igv.sam.AlignmentTrack.getBisulfiteContextPreContext | |
| 80 0.02% 97.50% 2 302012 org.broad.igv.sam.BisulfiteCounts.incrementCounts | |
| 81 0.02% 97.53% 2 302018 org.broad.igv.util.ObjectCache.put | |
| 82 0.02% 97.55% 2 302022 net.sf.samtools.SAMBinaryTagAndValue.insert | |
| 83 0.02% 97.57% 2 302051 net.sf.samtools.util.StringUtil.bytesToString | |
| 84 0.01% 97.58% 1 300018 java.util.jar.Manifest.read | |
| 85 0.01% 97.59% 1 300061 java.util.regex.Pattern$CharPropertyNames.defCtype | |
| 86 0.01% 97.60% 1 300104 java.util.Arrays.copyOfRange | |
| 87 0.01% 97.61% 1 300105 java.util.Arrays.copyOf | |
| 88 0.01% 97.62% 1 300106 sun.security.util.ManifestDigester.<init> | |
| 89 0.01% 97.63% 1 300132 java.lang.Class.forName0 | |
| 90 0.01% 97.65% 1 300161 sun.security.x509.CertificateX509Key.<init> | |
| 91 0.01% 97.66% 1 300210 sun.text.normalizer.NormalizerBase.<clinit> | |
| 92 0.01% 97.67% 1 300248 sun.security.provider.SHA.implCompress | |
| 93 0.01% 97.68% 1 300249 sun.misc.Unsafe.getInt | |
| 94 0.01% 97.69% 1 300250 sun.security.provider.DigestBase.engineUpdate | |
| 95 0.01% 97.70% 1 300259 java.util.Hashtable.put | |
| 96 0.01% 97.71% 1 300297 java.util.HashMap.<init> | |
| 97 0.01% 97.72% 1 300298 java.util.HashMap$HashIterator.<init> | |
| 98 0.01% 97.73% 1 300300 java.util.jar.JarFile.getBytes | |
| 99 0.01% 97.74% 1 300302 java.util.Hashtable.rehash | |
| 100 0.01% 97.76% 1 300310 java.beans.Introspector.instantiate | |
| 101 0.01% 97.77% 1 300367 java.lang.Package.getSystemPackage | |
| 102 0.01% 97.78% 1 300439 com.sun.org.apache.xerces.internal.parsers.XML11Configuration.<init> | |
| 103 0.01% 97.79% 1 300501 com.sun.org.apache.xerces.internal.dom.DeferredDocumentImpl.getNodeObject | |
| 104 0.01% 97.80% 1 300551 javax.swing.UIManager$LAFState.<init> | |
| 105 0.01% 97.81% 1 300618 sun.font.FontManager.getFCLocaleStr | |
| 106 0.01% 97.82% 1 300658 sun.nio.ch.FileChannelImpl.read | |
| 107 0.01% 97.83% 1 300700 sun.java2d.SurfaceData.<clinit> | |
| 108 0.01% 97.84% 1 300746 sun.awt.X11.XlibWrapper.XKeysymToKeycode | |
| 109 0.01% 97.85% 1 300767 javax.naming.CompositeName.<init> | |
| 110 0.01% 97.86% 1 300776 java.lang.UNIXProcess.forkAndExec | |
| 111 0.01% 97.88% 1 300806 javax.swing.UIManager.initialize | |
| 112 0.01% 97.89% 1 300829 java.util.zip.InflaterInputStream.<init> | |
| 113 0.01% 97.90% 1 300880 sun.awt.image.PNGImageDecoder.<clinit> | |
| 114 0.01% 97.91% 1 300895 com.jidesoft.plaf.LookAndFeelFactory.installJideExtension | |
| 115 0.01% 97.92% 1 300965 java.awt.image.ColorModel.getLinearRGB16TosRGB8LUT | |
| 116 0.01% 97.93% 1 300966 java.lang.StrictMath.floor | |
| 117 0.01% 97.94% 1 300969 java.io.RandomAccessFile.readBytes | |
| 118 0.01% 97.95% 1 300971 sun.security.ssl.SunJSSE.registerAlgorithms | |
| 119 0.01% 97.96% 1 300989 org.broad.igv.ui.IGV.<init> | |
| 120 0.01% 97.97% 1 301003 java.util.zip.ZipFile.freeEntry | |
| 121 0.01% 97.99% 1 301005 java.lang.Throwable.fillInStackTrace | |
| 122 0.01% 98.00% 1 301006 java.util.zip.ZipEntry.initFields | |
| 123 0.01% 98.01% 1 301042 sun.awt.image.GifImageDecoder.parseImage | |
| 124 0.01% 98.02% 1 301051 sun.awt.X11.XlibWrapper.XAllocColor | |
| 125 0.01% 98.03% 1 301099 java.awt.datatransfer.DataFlavor.<clinit> | |
| 126 0.01% 98.04% 1 301121 javax.swing.AbstractButton.updateDisplayedMnemonicIndex | |
| 127 0.01% 98.05% 1 301203 javax.swing.text.AbstractDocument.<init> | |
| 128 0.01% 98.06% 1 301239 javax.swing.AbstractButton.addChangeListener | |
| 129 0.01% 98.07% 1 301245 java.lang.Class$MethodArray.addIfNotPresent | |
| 130 0.01% 98.08% 1 301246 java.lang.reflect.Array.newArray | |
| 131 0.01% 98.09% 1 301247 java.util.concurrent.locks.AbstractQueuedSynchronizer.compareAndSetState | |
| 132 0.01% 98.11% 1 301248 java.lang.Throwable.fillInStackTrace | |
| 133 0.01% 98.12% 1 301249 java.util.ArrayList.<init> | |
| 134 0.01% 98.13% 1 301252 sun.reflect.ByteVectorImpl.<init> | |
| 135 0.01% 98.14% 1 301254 sun.misc.Resource.getBytes | |
| 136 0.01% 98.15% 1 301257 com.jidesoft.swing.JideSplitPane.createSplitPaneDivider | |
| 137 0.01% 98.16% 1 301259 java.lang.Class.newInstance0 | |
| 138 0.01% 98.17% 1 301274 java.lang.Object.getClass | |
| 139 0.01% 98.18% 1 301280 java.lang.Object.clone | |
| 140 0.01% 98.19% 1 301285 com.sun.org.apache.xerces.internal.impl.dtd.XMLSimpleType.setValues | |
| 141 0.01% 98.20% 1 301286 java.lang.String.indexOf | |
| 142 0.01% 98.22% 1 301287 java.util.Vector.<init> | |
| 143 0.01% 98.23% 1 301288 com.sun.org.apache.xerces.internal.util.SymbolTable$Entry.<init> | |
| 144 0.01% 98.24% 1 301307 com.sun.xml.internal.bind.DatatypeConverterImpl.<clinit> | |
| 145 0.01% 98.25% 1 301391 com.sun.xml.internal.bind.v2.model.impl.RuntimeModelBuilder.createClassInfo | |
| 146 0.01% 98.26% 1 301442 java.io.ByteArrayOutputStream.size | |
| 147 0.01% 98.27% 1 301530 com.sun.xml.internal.bind.v2.runtime.unmarshaller.UnmarshallerImpl.unmarshal0 | |
| 148 0.01% 98.28% 1 301545 java.awt.Component.repaint | |
| 149 0.01% 98.29% 1 301549 sun.awt.X11.XWindowPeer.<init> | |
| 150 0.01% 98.30% 1 301587 sun.awt.X11.XBaseWindow.getHints | |
| 151 0.01% 98.31% 1 301611 sun.awt.X11.XSelection.<init> | |
| 152 0.01% 98.32% 1 301641 java.lang.Object.clone | |
| 153 0.01% 98.34% 1 301642 java.awt.EventQueue.coalesceEvent | |
| 154 0.01% 98.35% 1 301655 sun.awt.X11.XlibWrapper.XFlush | |
| 155 0.01% 98.36% 1 301683 sun.awt.X11.XlibWrapper.XWindowEvent | |
| 156 0.01% 98.37% 1 301750 java.net.AbstractPlainSocketImpl.getOutputStream | |
| 157 0.01% 98.38% 1 301765 java.io.BufferedReader.readLine | |
| 158 0.01% 98.39% 1 301768 sun.awt.X11.XlibWrapper.XQueryTree | |
| 159 0.01% 98.40% 1 301771 java.lang.System.nanoTime | |
| 160 0.01% 98.41% 1 301778 com.google.common.util.concurrent.ExecutionList.<init> | |
| 161 0.01% 98.42% 1 301783 java.security.AccessController.getStackAccessControlContext | |
| 162 0.01% 98.43% 1 301799 sun.awt.X11.XlibWrapper.XSync | |
| 163 0.01% 98.45% 1 301803 sun.java2d.loops.MaskBlit.MaskBlit | |
| 164 0.01% 98.46% 1 301807 java.util.HashMap.putForCreate | |
| 165 0.01% 98.47% 1 301809 sun.security.util.ManifestDigester.<init> | |
| 166 0.01% 98.48% 1 301810 sun.security.util.ManifestDigester.<init> | |
| 167 0.01% 98.49% 1 301811 java.math.BigInteger.primitiveLeftShift | |
| 168 0.01% 98.50% 1 301812 java.util.Hashtable.get | |
| 169 0.01% 98.51% 1 301813 java.util.HashMap.<init> | |
| 170 0.01% 98.52% 1 301814 java.math.BigInteger.subN | |
| 171 0.01% 98.53% 1 301820 sun.java2d.loops.GraphicsPrimitive.makeUniqueID | |
| 172 0.01% 98.54% 1 301821 java.awt.Container.mixOnValidating | |
| 173 0.01% 98.55% 1 301822 java.lang.Throwable.fillInStackTrace | |
| 174 0.01% 98.57% 1 301823 net.sf.samtools.SAMFileHeader.<init> | |
| 175 0.01% 98.58% 1 301825 java.util.Hashtable.get | |
| 176 0.01% 98.59% 1 301828 java.security.AccessController.getStackAccessControlContext | |
| 177 0.01% 98.60% 1 301829 javax.swing.text.GapContent.insertString | |
| 178 0.01% 98.61% 1 301839 java.awt.Component.enable | |
| 179 0.01% 98.62% 1 301840 java.text.DontCareFieldPosition.getFieldDelegate | |
| 180 0.01% 98.63% 1 301841 javax.swing.plaf.basic.BasicComboBoxRenderer.getPreferredSize | |
| 181 0.01% 98.64% 1 301848 java.io.StreamTokenizer.nextToken | |
| 182 0.01% 98.65% 1 301854 java.nio.ByteBufferAsShortBufferB.ix | |
| 183 0.01% 98.66% 1 301857 java.nio.ByteBufferAsShortBufferB.ix | |
| 184 0.01% 98.67% 1 301858 org.broad.igv.sam.BaseAlignmentCounts.<init> | |
| 185 0.01% 98.69% 1 301859 net.sf.samtools.util.BlockCompressedInputStream.getFilePointer | |
| 186 0.01% 98.70% 1 301860 net.sf.samtools.util.BinaryCodec.readBytes | |
| 187 0.01% 98.71% 1 301862 java.util.ArrayList.<init> | |
| 188 0.01% 98.72% 1 301866 net.sf.samtools.BAMRecordCodec.decode | |
| 189 0.01% 98.73% 1 301867 net.sf.samtools.BAMFileReader$BAMQueryFilteringIterator.advance | |
| 190 0.01% 98.74% 1 301868 java.lang.Integer.intValue | |
| 191 0.01% 98.75% 1 301869 net.sf.samtools.BAMRecordCodec.decode | |
| 192 0.01% 98.76% 1 301872 java.lang.Object.hashCode | |
| 193 0.01% 98.77% 1 301874 net.sf.samtools.util.StringUtil.bytesToString | |
| 194 0.01% 98.78% 1 301876 java.lang.System.arraycopy | |
| 195 0.01% 98.80% 1 301878 org.broad.igv.sam.SamAlignment.createAlignmentBlocks | |
| 196 0.01% 98.81% 1 301879 net.sf.samtools.BAMRecord.decodeReadName | |
| 197 0.01% 98.82% 1 301881 net.sf.samtools.CigarElement.getLength | |
| 198 0.01% 98.83% 1 301882 org.broad.igv.sam.BisulfiteCounts.incrementCounts | |
| 199 0.01% 98.84% 1 301883 net.sf.samtools.BAMFileReader$BAMQueryFilteringIterator.next | |
| 200 0.01% 98.85% 1 301885 org.broad.igv.sam.ReadMate.<init> | |
| 201 0.01% 98.86% 1 301886 net.sf.samtools.SAMRecord.getMappingQuality | |
| 202 0.01% 98.87% 1 301887 org.broad.igv.sam.SamAlignment.getFlowSignalsStart | |
| 203 0.01% 98.88% 1 301888 org.broad.igv.sam.PEStats.update | |
| 204 0.01% 98.89% 1 301889 org.broad.igv.sam.AlignmentTileLoader.loadTile | |
| 205 0.01% 98.90% 1 301890 org.broad.igv.sam.SamAlignment.<init> | |
| 206 0.01% 98.92% 1 301892 org.broad.igv.sam.SamAlignment.<init> | |
| 207 0.01% 98.93% 1 301894 javax.swing.JComponent.getFlag | |
| 208 0.01% 98.94% 1 301897 org.broad.igv.sam.AlignmentTrack.getBisulfiteContextPostContext | |
| 209 0.01% 98.95% 1 301900 java.lang.Thread.currentThread | |
| 210 0.01% 98.96% 1 301907 net.sf.samtools.util.BlockGunzipper.unzipBlock | |
| 211 0.01% 98.97% 1 301910 org.broad.igv.sam.AlignmentBlock.getStart | |
| 212 0.01% 98.98% 1 301913 javax.swing.JComponent.setFlag | |
| 213 0.01% 98.99% 1 301914 java.util.LinkedHashMap.addEntry | |
| 214 0.01% 99.00% 1 301917 java.lang.Integer.getChars | |
| 215 0.01% 99.01% 1 301919 java.awt.geom.Path2D$Float.append | |
| 216 0.01% 99.03% 1 301920 org.broad.igv.sam.AlignmentTileLoader$AlignmentTile.addRecord | |
| 217 0.01% 99.04% 1 301924 java.util.TaskQueue.getMin | |
| 218 0.01% 99.05% 1 301926 net.sf.samtools.SAMBinaryTagAndValue.find | |
| 219 0.01% 99.06% 1 301928 net.sf.samtools.BAMRecord.decodeReadBases | |
| 220 0.01% 99.07% 1 301929 java.lang.StringBuffer.toString | |
| 221 0.01% 99.08% 1 301931 java.awt.Component.getGraphicsConfiguration | |
| 222 0.01% 99.09% 1 301933 org.apache.commons.math.stat.descriptive.moment.Variance.<init> | |
| 223 0.01% 99.10% 1 301934 org.apache.commons.math.util.FastMath.quadMult | |
| 224 0.01% 99.11% 1 301935 org.apache.commons.math.util.FastMath.slowexp | |
| 225 0.01% 99.12% 1 301936 org.apache.commons.math.util.FastMath.slowLog | |
| 226 0.01% 99.13% 1 301937 java.awt.Component.getGraphicsConfiguration | |
| 227 0.01% 99.15% 1 301938 java.util.Arrays.mergeSort | |
| 228 0.01% 99.16% 1 301939 java.util.Arrays.mergeSort | |
| 229 0.01% 99.17% 1 301940 java.util.ArrayList.set | |
| 230 0.01% 99.18% 1 301941 java.util.Arrays.copyOf | |
| 231 0.01% 99.19% 1 301942 org.broad.igv.sam.AlignmentPacker.pack | |
| 232 0.01% 99.20% 1 301952 sun.misc.Unsafe.compareAndSwapInt | |
| 233 0.01% 99.21% 1 301954 sun.java2d.pipe.PixelToParallelogramConverter.fillRectangle | |
| 234 0.01% 99.22% 1 301955 org.broad.igv.sam.CoverageTrack.drawBar | |
| 235 0.01% 99.23% 1 301966 java.text.NumberFormat.getMinimumIntegerDigits | |
| 236 0.01% 99.24% 1 301970 org.broad.igv.sam.AlignmentRenderer.drawBase | |
| 237 0.01% 99.26% 1 301971 sun.java2d.x11.X11Renderer.XFillRect | |
| 238 0.01% 99.27% 1 301972 java.lang.Thread.currentThread | |
| 239 0.01% 99.28% 1 301973 org.broad.igv.sam.AlignmentRenderer.drawBase | |
| 240 0.01% 99.29% 1 301977 sun.java2d.x11.X11SurfaceData.validatePipe | |
| 241 0.01% 99.30% 1 301978 org.broad.igv.sam.AlignmentRenderer.renderAlignments | |
| 242 0.01% 99.31% 1 301980 org.broad.igv.sam.AlignmentBlock.getStart | |
| 243 0.01% 99.32% 1 301981 java.lang.Integer.hashCode | |
| 244 0.01% 99.33% 1 301982 java.lang.Thread.currentThread | |
| 245 0.01% 99.34% 1 301983 java.lang.StrictMath.ceil | |
| 246 0.01% 99.35% 1 301984 java.util.Hashtable.containsKey | |
| 247 0.01% 99.36% 1 301985 java.lang.System.arraycopy | |
| 248 0.01% 99.38% 1 301989 sun.java2d.x11.X11Renderer.XDoPath | |
| 249 0.01% 99.39% 1 301993 java.util.regex.Matcher.<init> | |
| 250 0.01% 99.40% 1 301994 sun.java2d.pisces.PiscesCache.addTupleToRow | |
| 251 0.01% 99.41% 1 301998 sun.security.util.SignatureFileVerifier.updateSigners | |
| 252 0.01% 99.42% 1 301999 java.lang.String.lastIndexOf | |
| 253 0.01% 99.43% 1 302000 com.google.gson.stream.StringPool.get | |
| 254 0.01% 99.44% 1 302001 java.util.HashMap.put | |
| 255 0.01% 99.45% 1 302002 net.sf.samtools.BAMRecordCodec.decode | |
| 256 0.01% 99.46% 1 302003 java.util.ArrayList.iterator | |
| 257 0.01% 99.47% 1 302004 net.sf.samtools.util.BinaryCodec.readUByte | |
| 258 0.01% 99.49% 1 302005 net.sf.samtools.BAMRecordCodec.decode | |
| 259 0.01% 99.50% 1 302006 org.broad.igv.sam.AbstractAlignment.getReadName | |
| 260 0.01% 99.51% 1 302007 org.broad.igv.sam.AlignmentTileLoader.loadTile | |
| 261 0.01% 99.52% 1 302008 org.broad.igv.sam.AlignmentTileLoader.loadTile | |
| 262 0.01% 99.53% 1 302009 javax.swing.JComponent.paint | |
| 263 0.01% 99.54% 1 302013 javax.swing.JComponent.paintChildren | |
| 264 0.01% 99.55% 1 302014 org.broad.igv.sam.AlignmentTileLoader$AlignmentTile.emptyBucket | |
| 265 0.01% 99.56% 1 302016 java.util.HashMap.size | |
| 266 0.01% 99.57% 1 302019 java.lang.Object.hashCode | |
| 267 0.01% 99.58% 1 302021 net.sf.samtools.util.BlockCompressedInputStream.readBlock | |
| 268 0.01% 99.59% 1 302023 sun.font.FontManager.getFont2D | |
| 269 0.01% 99.61% 1 302025 java.util.Arrays.mergeSort | |
| 270 0.01% 99.62% 1 302026 sun.java2d.pipe.AlphaColorPipe.renderPathTile | |
| 271 0.01% 99.63% 1 302031 java.lang.String.toCharArray | |
| 272 0.01% 99.64% 1 302032 sun.misc.Unsafe.getFloat | |
| 273 0.01% 99.65% 1 302033 java.lang.Integer.hashCode | |
| 274 0.01% 99.66% 1 302034 org.broad.igv.PreferenceManager.getAsInt | |
| 275 0.01% 99.67% 1 302035 java.awt.Color.hashCode | |
| 276 0.01% 99.68% 1 302036 org.broad.igv.sam.AlignmentRenderer.drawAlignment | |
| 277 0.01% 99.69% 1 302037 sun.java2d.pisces.Helpers.widenArray | |
| 278 0.01% 99.70% 1 302038 sun.font.GlyphList.getInstance | |
| 279 0.01% 99.72% 1 302039 org.broad.igv.sam.AlignmentTrack.renderAlignments | |
| 280 0.01% 99.73% 1 302040 sun.java2d.SunGraphics2D.validateBasicStroke | |
| 281 0.01% 99.74% 1 302041 java.awt.Container.getComponent | |
| 282 0.01% 99.75% 1 302042 java.awt.Container.addImpl | |
| 283 0.01% 99.76% 1 302043 net.sf.samtools.BAMRecordCodec.decode | |
| 284 0.01% 99.77% 1 302044 net.sf.samtools.BAMRecordCodec.decode | |
| 285 0.01% 99.78% 1 302045 org.broad.igv.feature.genome.SequenceWrapper.getSequenceTile | |
| 286 0.01% 99.79% 1 302046 org.broad.igv.feature.genome.SequenceWrapper.getSequenceTile | |
| 287 0.01% 99.80% 1 302047 java.util.HashMap.get | |
| 288 0.01% 99.81% 1 302048 javax.swing.JComponent.getInsets | |
| 289 0.01% 99.82% 1 302049 sun.java2d.x11.XSurfaceData.XSetClip | |
| 290 0.01% 99.84% 1 302050 java.util.Hashtable.size | |
| 291 0.01% 99.85% 1 302052 org.broad.igv.sam.AlignmentTileLoader$AlignmentTile.addRecord | |
| 292 0.01% 99.86% 1 302053 net.sf.samtools.BinaryTagCodec.readSingleValue | |
| 293 0.01% 99.87% 1 302054 org.broad.igv.sam.SamAlignment.getReadSequence | |
| 294 0.01% 99.88% 1 302055 org.broad.igv.sam.AlignmentTileLoader.loadTile | |
| 295 0.01% 99.89% 1 302056 org.broad.igv.PreferenceManager.getAsBoolean | |
| 296 0.01% 99.90% 1 302057 org.broad.igv.sam.BaseAlignmentCounts.incCounts | |
| 297 0.01% 99.91% 1 302058 org.broad.igv.sam.AlignmentTileLoader.loadTile | |
| 298 0.01% 99.92% 1 302059 sun.java2d.x11.X11SurfaceData.getBlitGC | |
| 299 0.01% 99.93% 1 302060 org.broad.igv.sam.AlignmentTileLoader$AlignmentTile$SamplingBucket.<init> | |
| 300 0.01% 99.95% 1 302061 javax.swing.RepaintManager.addDirtyRegion0 | |
| 301 0.01% 99.96% 1 302062 java.lang.Object.getClass | |
| 302 0.01% 99.97% 1 302063 org.broad.igv.sam.AbstractAlignment.getMappingQuality | |
| 303 0.01% 99.98% 1 302064 java.lang.StrictMath.floor | |
| 304 0.01% 99.99% 1 302065 org.broad.igv.sam.AlignmentRenderer.drawAlignment | |
| 305 0.01% 100.00% 1 302066 sun.java2d.loops.MaskBlit.MaskBlit | |
| CPU SAMPLES END |
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| load all.bam | |
| collapse | |
| goto chr1:8419-12584 | |
| goto chr5:273379-273513 | |
| goto chr10:704391-712470 | |
| exit |
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| Dataset is simply a bam file of aligned reads | |
| command used to do profiling was | |
| java -agentlib:hprof=cpu=samples,interval=20,depth=3 -Dapple.laf.useScreenMenuBar=true -Xmx15750m -jar IGV_2.1.24/igv.jar -b script.igv | |
| java version "1.6.0_22" | |
| OpenJDK Runtime Environment (IcedTea6 1.10.6) (rhel-1.25.1.10.6.el5_8-x86_64) | |
| OpenJDK 64-Bit Server VM (build 20.0-b11, mixed mode) |
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