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refseq annotation rod is now manually bound to tell coding indels from non-coding ones 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1001 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-06-12 19:27:37 +00:00
parent 260fd0dc45
commit ca09a10b76
1 changed files with 39 additions and 5 deletions
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44
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java
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@ -14,8 +14,12 @@ import net.sf.samtools.SAMFileReader;
import net.sf.samtools.SAMReadGroupRecord;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.refdata.RODIterator;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
import org.broadinstitute.sting.gatk.refdata.rodRefSeq;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.playground.utils.CircularArray;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.cmdLine.Argument;
@ -48,6 +52,9 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
private int currentContigIndex = -1;
private String refName = null;
private java.io.Writer output = null;
private GenomeLoc location = null;
private RODIterator<rodRefSeq> refseqIterator;
private Set<String> normal_samples = new HashSet<String>();
private Set<String> tumor_samples = new HashSet<String>();
@ -56,8 +63,14 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
public void initialize() {
coverage = new RunningCoverage(0,WINDOW_SIZE);
ReferenceOrderedData<rodRefSeq> refseq = new ReferenceOrderedData<rodRefSeq>("refseq",
new java.io.File("/humgen/gsa-scr1/GATK_Data/refGene.sorted.txt"),rodRefSeq.class);
refseqIterator = refseq.iterator();
int nSams = getToolkit().getArguments().samFiles.size();
location = new GenomeLoc(0,1);
if ( call_somatic ) {
if ( nSams != 2 ) {
@ -146,13 +159,17 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
else emit(1000000000);
currentContigIndex = read.getReferenceIndex();
refName = new String(read.getReferenceName());
location.setContig(refName);
coverage.clear(); // reset coverage window; this will also set reference position to 0
if ( call_somatic) normal_coverage.clear();
}
if ( read.getAlignmentStart() < coverage.getStart() ) {
// should never happen
throw new StingException("Read "+read.getReadName()+": out of order on the contig");
throw new StingException("Read "+read.getReadName()+": out of order on the contig\n"+
"Read starts at "+read.getReferenceName()+":"+read.getAlignmentStart()+ " (cigar="+read.getCigarString()+
"); window starts at "+coverage.getStart());
}
// a little trick here: we want to make sure that current read completely fits into the current
@ -269,6 +286,7 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
for ( long pos = coverage.getStart() ; pos < Math.min(position,coverage.getStop()+1) ; pos++ ) {
List<IndelVariant> tumor_variants = coverage.indelsAt(pos);
List<IndelVariant> normal_variants = normal_coverage.indelsAt(pos);
@ -281,6 +299,10 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
if ( tumor_cov < minCoverage ) continue; // low coverage
if ( normal_cov < minNormalCoverage ) continue; // low coverage
location.setStart(pos); location.setStop(pos); // retrieve annotation data
rodRefSeq annotation = refseqIterator.seekForward(location);
int total_variant_count_tumor = 0;
int max_variant_count_tumor = 0;
String indelStringTumor = null;
@ -298,22 +320,34 @@ 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 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;
if ( normal_variants.size() == 0 ) {
try {
output.write(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+"\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");
}
message += "\tSOMATIC";
message += "\tSOMATIC\t";
} else {
message += "\tGERMLINE";
message += "\tGERMLINE\t";
}
message += annotationString;
if ( verbose ) System.out.println(message);
}
// for ( IndelVariant var : variants ) {