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bug: printing incorrect coordinates into output, finally fixed (?) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1017 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-06-16 18:08:56 +00:00
parent 647b8a1ab0
commit 010304fe44
1 changed files with 22 additions and 12 deletions
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34
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java
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@ -155,11 +155,18 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
return -1; return -1;
} }
// if ( read.getAlignmentStart() < 112337549 && read.getAlignmentEnd() > 112337550 ) {
// System.out.print("adding "+read.getReadString()+" "+read.getCigarString());
// }
if ( read.getReadUnmappedFlag() || if ( read.getReadUnmappedFlag() ||
read.getDuplicateReadFlag() || read.getDuplicateReadFlag() ||
read.getNotPrimaryAlignmentFlag() || read.getNotPrimaryAlignmentFlag() ||
read.getMappingQuality() == 0 ) return 0; // we do not need those reads! read.getMappingQuality() == 0 ) {
// System.out.println(" ignored");
return 0; // we do not need those reads!
}
// System.out.print(" added");
if ( read.getReferenceIndex() != currentContigIndex ) { if ( read.getReferenceIndex() != currentContigIndex ) {
// we just jumped onto a new contig // we just jumped onto a new contig
@ -227,8 +234,10 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
if ( rg == null ) throw new StingException("Read "+read.getReadName()+" has no read group in merged stream"); if ( rg == null ) throw new StingException("Read "+read.getReadName()+" has no read group in merged stream");
if ( normal_samples.contains(rg) ) { if ( normal_samples.contains(rg) ) {
// System.out.println(" TO NORMAL");
normal_coverage.add(read,ref); normal_coverage.add(read,ref);
} else if ( tumor_samples.contains(rg) ) { } else if ( tumor_samples.contains(rg) ) {
// System.out.println(" TO TUMOR");
coverage.add(read,ref); coverage.add(read,ref);
} else { } else {
throw new StingException("Unrecognized read group in merged stream: "+rg); throw new StingException("Unrecognized read group in merged stream: "+rg);
@ -404,14 +413,15 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
if ( (double)total_variant_count_tumor > minFraction * tumor_cov && (double) max_variant_count_tumor > minConsensusFraction*total_variant_count_tumor ) { if ( (double)total_variant_count_tumor > minFraction * tumor_cov && (double) max_variant_count_tumor > minConsensusFraction*total_variant_count_tumor ) {
String annotationString = getAnnotationString(annotation); String annotationString = getAnnotationString(annotation);
/*
int leftpos = pos-1; long leftpos = pos;
int rightpos = pos-1; long rightpos = pos+event_length_tumor-1;
if ( event_length_tumor > 0 ) { if ( event_length_tumor == 0 ) { // insertion
leftpos -= event_length; leftpos--;
rightpos = leftpos;
} }
*/
String message = refName+"\t"+(pos-1)+"\t"+(event_length_tumor > 0 ? pos-1+event_length_tumor : pos-1)+ String message = refName+"\t"+leftpos+"\t"+rightpos+
"\t"+(event_length_tumor >0? "-":"+")+indelStringTumor +":"+total_variant_count_tumor+"/"+tumor_cov; "\t"+(event_length_tumor >0? "-":"+")+indelStringTumor +":"+total_variant_count_tumor+"/"+tumor_cov;
if ( normal_variants.size() == 0 ) { if ( normal_variants.size() == 0 ) {
@ -434,8 +444,8 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
// } // }
} }
coverage.shift((int)(position - coverage.getStart() ) ); coverage.shift((int)(stop_at - coverage.getStart() ) );
normal_coverage.shift((int)(position - normal_coverage.getStart() ) ); normal_coverage.shift((int)(stop_at - normal_coverage.getStart() ) );
} }
@ -505,7 +515,7 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
*/ */
public int lengthOnRef() { public int lengthOnRef() {
if ( type == Type.D ) return bases.length(); if ( type == Type.D ) return bases.length();
else return -1; else return 0;
} }
public void increment() { count+=1; } public void increment() { count+=1; }