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not crashing when refseq annotation track is not requested is a nice added feature 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1079 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-06-23 22:52:40 +00:00
parent eb999f880a
commit dfa2efbcf5
1 changed files with 4 additions and 4 deletions
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8
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java
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@ -316,7 +316,7 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
} }
location.setStart(pos); location.setStop(pos); // retrieve annotation data location.setStart(pos); location.setStop(pos); // retrieve annotation data
rodRefSeq annotation = refseqIterator.seekForward(location); rodRefSeq annotation = (refseqIterator == null ? null : refseqIterator.seekForward(location));
int total_variant_count = 0; int total_variant_count = 0;
int max_variant_count = 0; int max_variant_count = 0;
@ -334,7 +334,7 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
} }
if ( (double)total_variant_count > minFraction * cov && (double) max_variant_count > minConsensusFraction*total_variant_count ) { if ( (double)total_variant_count > minFraction * cov && (double) max_variant_count > minConsensusFraction*total_variant_count ) {
String annotationString = getAnnotationString(annotation); String annotationString = (refseqIterator == null ? "" : getAnnotationString(annotation));
String message = refName+"\t"+(pos-1)+"\t"+(event_length > 0 ? pos-1+event_length : pos-1)+ String message = refName+"\t"+(pos-1)+"\t"+(event_length > 0 ? pos-1+event_length : pos-1)+
"\t"+(event_length>0? "-":"+")+indelString +":"+total_variant_count+"/"+cov; "\t"+(event_length>0? "-":"+")+indelString +":"+total_variant_count+"/"+cov;
@ -413,7 +413,7 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
continue; // too dirty continue; // too dirty
} }
location.setStart(pos); location.setStop(pos); // retrieve annotation data location.setStart(pos); location.setStop(pos); // retrieve annotation data
rodRefSeq annotation = refseqIterator.seekForward(location); rodRefSeq annotation = (refseqIterator == null ? null : refseqIterator.seekForward(location));
int total_variant_count_tumor = 0; int total_variant_count_tumor = 0;
@ -433,7 +433,7 @@ 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 = ( refseqIterator == null ? "": getAnnotationString(annotation));
long leftpos = pos; long leftpos = pos;
long rightpos = pos+event_length_tumor-1; long rightpos = pos+event_length_tumor-1;