Patch for http://sv.gersteinlab.org/cnvnator/ including the black6 genome

cnvnator_mouse.patch

Only in ./: cnvnator
diff -u ../../../CNVnator_v0.3/src/cnvnator.cpp ./cnvnator.cpp
--- ../../../CNVnator_v0.3/src/cnvnator.cpp	2014-02-01 20:29:35.000000000 -0800
+++ ./cnvnator.cpp	2014-07-21 13:06:23.022155584 -0700
@@ -39,7 +39,7 @@
   usage += argv[0];
   usage += " -pe   file1.bam ... -qual val(20) -over val(0.8) [-f file]\n";
   usage += "\n";
-  usage += "Valid genomes (-genome option) are: NCBI36, hg18, GRCh37, hg19\n";
+  usage += "Valid genomes (-genome option) are: NCBI36, hg18, GRCh37, hg19, black6\n";
 
   if (argc < 2) {
     cerr<<"Not enough parameters."<<endl;
Only in ./: cnvnator_mouse.patch
diff -u ../../../CNVnator_v0.3/src/Genome.cpp ./Genome.cpp
--- ../../../CNVnator_v0.3/src/Genome.cpp	2014-02-01 20:29:35.000000000 -0800
+++ ./Genome.cpp	2014-07-21 13:54:34.917484815 -0700
@@ -63,6 +63,32 @@
     cnames_[21] = "chr22"; clens_[21] =  51304566;
     cnames_[22] =  "chrX"; clens_[22] = 155270560;
     cnames_[23] =  "chrY"; clens_[23] =  59373566;
+   } else if (name == "black6") {
+    gname_       = "black6";
+    other_gname_ = "mouse";
+    n_chr_      = 22;
+    cnames_[0]  = "chr1";  clens_[0]  = 197195432;
+    cnames_[1]  = "chr2";  clens_[1]  = 181748087;
+    cnames_[2]  = "chr3";  clens_[2]  = 159599783;
+    cnames_[3]  = "chr4";  clens_[3]  = 155630120;
+    cnames_[4]  = "chr5";  clens_[4]  = 152537259;
+    cnames_[5]  = "chr6";  clens_[5]  = 149517037;
+    cnames_[6]  = "chr7";  clens_[6]  = 152524553;
+    cnames_[7]  = "chr8";  clens_[7]  = 131738871;
+    cnames_[8]  = "chr9";  clens_[8]  = 124076172;
+    cnames_[9]  = "chr10"; clens_[9]  = 129993255;
+    cnames_[10] = "chr11"; clens_[10] = 121843856;
+    cnames_[11] = "chr12"; clens_[11] = 121257530;
+    cnames_[12] = "chr13"; clens_[12] = 120284312;
+    cnames_[13] = "chr14"; clens_[13] = 125194864;
+    cnames_[14] = "chr15"; clens_[14] = 103494974;
+    cnames_[15] = "chr16"; clens_[15] = 98319150;
+    cnames_[16] = "chr17"; clens_[16] = 95272651;
+    cnames_[17] = "chr18"; clens_[17] = 90772031;
+    cnames_[18] = "chr19"; clens_[18] = 61342430;
+    cnames_[19] = "chrM"; clens_[19]  = 16299;
+    cnames_[20] = "chrX"; clens_[20]  = 166650296;
+    cnames_[21] = "chrY"; clens_[21]  = 15902555;
   } else {
     cerr<<"Unknown genome '"<<org_name<<"'."<<endl;
   }
diff -u ../../../CNVnator_v0.3/src/HisMaker.cpp ./HisMaker.cpp
--- ../../../CNVnator_v0.3/src/HisMaker.cpp	2014-02-01 20:29:35.000000000 -0800
+++ ./HisMaker.cpp	2014-07-21 13:06:23.022155584 -0700
@@ -2441,6 +2441,8 @@
     // Creating histograms with GC-content
     cout<<"Making GC histogram for '"<<chrom<<"' ..."<<endl;
     if (readChromosome(name,seq_buffer,org_len) != org_len) {
+      cerr<<readChromosome(name,seq_buffer,org_len)<<endl;
+      cerr<<org_len<<endl;
       cerr<<"Read sequence is of different length from expectation."<<endl;
       cerr<<"Doing nothing."<<endl;
     } else {
diff -u ../../../CNVnator_v0.3/src/Makefile ./Makefile
--- ../../../CNVnator_v0.3/src/Makefile	2014-02-01 20:29:35.000000000 -0800
+++ ./Makefile	2014-07-21 13:06:23.022155584 -0700
@@ -1,15 +1,13 @@
 VERSION	  = v0.3
-#ROOTFLAGS = -pthread -m64
-ROOTFLAGS = -m64
+ROOTFLAGS = -pthread -m64
 LIBS      = -lz
-ROOTLIBS  = -L$(ROOTSYS)/lib -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d \
+ROOTLIBS  = -L/usr/lib -L/usr/lib/root -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d \
 		-lGpad -lTree -lRint -lMatrix -lPhysics \
 		-lMathCore -lThread -lGui
 
 CXX    = g++ $(ROOTFLAGS) -DCNVNATOR_VERSION=\"$(VERSION)\"
-SAMDIR = samtools
-INC    = -I$(ROOTSYS)/include -I$(SAMDIR)
-SAMLIB = $(SAMDIR)/libbam.a
+INC    = -I/usr/include -I/usr/include/root -I/usr/include/bam
+SAMLIB = /usr/lib/libbam.a
 
 OBJDIR = obj
 OBJS   = $(OBJDIR)/cnvnator.o  \
Only in ./: obj
Common subdirectories: ../../../CNVnator_v0.3/src/samtools and ./samtools