Having problems with the SortingCollection which seems to skip records. Created this gist to use for reference when e-mailing samtools-devel list.

DemoIteratorSkipsRecords.scala

package molmed

import net.sf.samtools.util.SortingCollection
import net.sf.samtools.BAMRecordCodec
import net.sf.picard.fastq.FastqRecord
import java.util.Comparator
import java.io.InputStream
import java.io.PrintStream
import net.sf.picard.fastq.FastqConstants

object DemoIteratorSkipsRecords extends App {

  val sortingCollection = SortingCollection.newInstance(
    classOf[FastqRecord],
    new FastqRecordCodec(), new FastqRecordComparator(),
    2)

  sortingCollection.add(new FastqRecord("a1", "AA", "", "55"))
  sortingCollection.add(new FastqRecord("a2", "AA", "", "55"))
  sortingCollection.add(new FastqRecord("a3", "AA", "", "55"))
  sortingCollection.add(new FastqRecord("a4", "AA", "", "55"))
  sortingCollection.add(new FastqRecord("a5", "AA", "", "55"))
  sortingCollection.add(new FastqRecord("a6", "AA", "", "55"))
  sortingCollection.add(new FastqRecord("a7", "AA", "", "55"))
  sortingCollection.add(new FastqRecord("a8", "AA", "", "55"))

  sortingCollection.doneAdding()

  val iterator = sortingCollection.iterator()
  while (iterator.hasNext()) {
    val rec = iterator.next()
    println("record=" + rec.getReadHeader())
  }

  class FastqRecordComparator extends Comparator[FastqRecord] {
    def compare(a: FastqRecord, b: FastqRecord): Int =
      a.getReadHeader().compareTo(b.getReadHeader())
  }

  class FastqRecordCodec extends SortingCollection.Codec[FastqRecord] {

    var writer: PrintStream = null
    var in: scala.io.BufferedSource = null
    
    def decode(): FastqRecord = {      
      val lines = in.getLines
      val fourLines = lines.take(4).toList
      if (fourLines.isEmpty)
        null
      else
        new FastqRecord(fourLines(0), fourLines(1), fourLines(2), fourLines(3))
    }

    def encode(rec: FastqRecord): Unit = {
      writer.print(FastqConstants.SEQUENCE_HEADER)
      writer.println(rec.getReadHeader())
      writer.println(rec.getReadString())
      writer.print(FastqConstants.QUALITY_HEADER)
      writer.println(if (rec.getBaseQualityHeader() == null) "" else rec.getBaseQualityHeader())
      writer.println(rec.getBaseQualityString())
    }

    def setInputStream(inputStream: java.io.InputStream): Unit = {
      this.in = scala.io.Source.fromInputStream(inputStream)
    }

    def setOutputStream(outputStream: java.io.OutputStream): Unit = {
      this.writer = new PrintStream(outputStream)
    }
  }

}

output.txt

This was the problematic first input, now it's working fine though.
record=@a1
record=@a3
record=@a5
record=@a7