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add refseq annotations to single sample calls 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1003 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-06-12 19:43:30 +00:00
parent e9be2a9c60
commit 811f560efb
1 changed files with 32 additions and 13 deletions
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45
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java
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@ -59,6 +59,13 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
private Set<String> normal_samples = new HashSet<String>();
private Set<String> tumor_samples = new HashSet<String>();
private static String annGenomic = "GENOMIC";
private static String annIntron = "INTRON";
private static String annUTR = "UTR";
private static String annCoding = "CODING";
private static String annUnknown = "UNKNOWN";
@Override
public void initialize() {
coverage = new RunningCoverage(0,WINDOW_SIZE);
@ -244,6 +251,9 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
if ( cov < minCoverage ) continue; // low coverage
location.setStart(pos); location.setStop(pos); // retrieve annotation data
rodRefSeq annotation = refseqIterator.seekForward(location);
int total_variant_count = 0;
int max_variant_count = 0;
String indelString = null;
@ -260,14 +270,19 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
}
if ( (double)total_variant_count > minFraction * cov && (double) max_variant_count > minConsensusFraction*total_variant_count ) {
String annotationString = getAnnotationString(annotation);
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;
try {
output.write(refName+"\t"+(pos-1)+"\t"+(event_length > 0 ? pos-1+event_length : pos-1)+
"\t"+(event_length>0? "-":"+")+indelString +":"+total_variant_count+"/"+cov+"\n");
output.write(message+"\n");
} catch (IOException e) {
System.out.println(e.getMessage());
e.printStackTrace();
throw new StingException("Error encountered while writing into output BED file");
}
if ( verbose ) System.out.println(message + "\t"+ annotationString);
}
// for ( IndelVariant var : variants ) {
// System.out.print("\t"+var.getType()+"\t"+var.getBases()+"\t"+var.getCount());
@ -320,17 +335,7 @@ 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 ) {
String annotationString = null;
if ( annotation == null ) annotationString = "GENOMIC";
else {
if ( annotation.isExon() ) {
if ( annotation.isCoding() ) annotationString = "CODING";
else annotationString = "UTR";
} else {
if ( annotation.isCoding() ) annotationString = "INTRON";
else annotationString = "UNKNOWN";
}
}
String annotationString = getAnnotationString(annotation);
String message = refName+"\t"+(pos-1)+"\t"+(event_length_tumor > 0 ? pos-1+event_length_tumor : pos-1)+
"\t"+(event_length_tumor >0? "-":"+")+indelStringTumor +":"+total_variant_count_tumor+"/"+tumor_cov;
@ -359,6 +364,20 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
normal_coverage.shift((int)(position - normal_coverage.getStart() ) );
}
private String getAnnotationString(rodRefSeq ann) {
if ( ann == null ) return annGenomic;
else {
if ( ann.isExon() ) {
if ( ann.isCoding() ) return annCoding;
else return annUTR;
} else {
if ( ann.isCoding() ) return annIntron;
else return annUnknown;
}
}
}
@Override
public void onTraversalDone(Integer result) {