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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> normal_samples = new HashSet<String>();
private Set<String> tumor_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 @Override
public void initialize() { public void initialize() {
coverage = new RunningCoverage(0,WINDOW_SIZE); coverage = new RunningCoverage(0,WINDOW_SIZE);
@ -244,6 +251,9 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
if ( cov < minCoverage ) continue; // low coverage 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 total_variant_count = 0;
int max_variant_count = 0; int max_variant_count = 0;
String indelString = null; 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 ) { 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 { try {
output.write(refName+"\t"+(pos-1)+"\t"+(event_length > 0 ? pos-1+event_length : pos-1)+ output.write(message+"\n");
"\t"+(event_length>0? "-":"+")+indelString +":"+total_variant_count+"/"+cov+"\n");
} catch (IOException e) { } catch (IOException e) {
System.out.println(e.getMessage()); System.out.println(e.getMessage());
e.printStackTrace(); e.printStackTrace();
throw new StingException("Error encountered while writing into output BED file"); throw new StingException("Error encountered while writing into output BED file");
} }
if ( verbose ) System.out.println(message + "\t"+ annotationString);
} }
// for ( IndelVariant var : variants ) { // for ( IndelVariant var : variants ) {
// System.out.print("\t"+var.getType()+"\t"+var.getBases()+"\t"+var.getCount()); // 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 ) { if ( (double)total_variant_count_tumor > minFraction * tumor_cov && (double) max_variant_count_tumor > minConsensusFraction*total_variant_count_tumor ) {
String annotationString = null; String annotationString = getAnnotationString(annotation);
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 message = refName+"\t"+(pos-1)+"\t"+(event_length_tumor > 0 ? pos-1+event_length_tumor : pos-1)+ 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; "\t"+(event_length_tumor >0? "-":"+")+indelStringTumor +":"+total_variant_count_tumor+"/"+tumor_cov;
@ -360,6 +365,20 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
} }
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 @Override
public void onTraversalDone(Integer result) { public void onTraversalDone(Integer result) {
emit(1000000000); // emit everything we might have left emit(1000000000); // emit everything we might have left