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Now uses rodRefSeq in its new reincarnation 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1698 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-09-23 18:19:36 +00:00
parent bf7cd66d53
commit fa87dd386d
1 changed files with 13 additions and 14 deletions
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27
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java
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@ -73,7 +73,7 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
private java.io.Writer output = null;
private GenomeLoc location = null;
private SeekableRODIterator<rodRefSeq> refseqIterator=null;
private SeekableRODIterator<rodRefSeq> refseqIterator=null;
private Set<String> normalReadGroups;
private Set<String> tumorReadGroups ;
@ -99,7 +99,7 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
if ( RefseqFileName != null ) {
ReferenceOrderedData<rodRefSeq> refseq = new ReferenceOrderedData<rodRefSeq>("refseq",
new java.io.File(RefseqFileName),rodRefSeq.class);
new java.io.File(RefseqFileName), rodRefSeq.class);
refseqIterator = refseq.iterator();
System.out.println("Using RefSeq annotations from "+RefseqFileName);
@ -416,11 +416,11 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
location = GenomeLocParser.setStart(location,pos); location = GenomeLocParser.setStop(location,pos); // retrieve annotation data
RODRecordList<rodRefSeq> annotationList = (refseqIterator == null ? null : refseqIterator.seekForward(location));
rodRefSeq annotation = ( annotationList == null ? null : annotationList.getRecords().get(0) ) ;
Pair<IndelVariant,Integer> p = findConsensus(variants);
if ( isCall(p,cov) ) {
String message = makeBedLine(p,cov,pos,output);
String annotationString = (refseqIterator == null ? "" : getAnnotationString(annotation));
String annotationString = (refseqIterator == null ? "" : getAnnotationString(annotationList));
if ( verbose ) out.println(message + "\t"+ annotationString);
}
@ -517,12 +517,11 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
}
location = GenomeLocParser.setStart(location,pos); location = GenomeLocParser.setStop(location,pos); // retrieve annotation data
RODRecordList<rodRefSeq> annotationList = (refseqIterator == null ? null : refseqIterator.seekForward(location));
rodRefSeq annotation = ( annotationList == null ? null : annotationList.getRecords().get(0) ) ;
Pair<IndelVariant,Integer> p_tumor = findConsensus(tumor_variants);
if ( isCall(p_tumor,tumor_cov) ) {
String message = makeBedLine(p_tumor,tumor_cov,pos);
String annotationString = (refseqIterator == null ? "" : getAnnotationString(annotation));
String annotationString = (refseqIterator == null ? "" : getAnnotationString(annotationList));
if ( normal_variants.size() == 0 ) {
@ -560,20 +559,20 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
}
private String getAnnotationString(rodRefSeq ann) {
private String getAnnotationString(RODRecordList<rodRefSeq> ann) {
if ( ann == null ) return annGenomic;
else {
StringBuilder b = new StringBuilder();
if ( ann.isExon() ) {
if ( ann.isCoding() ) b.append(annCoding);
else b.append(annUTR);
if ( rodRefSeq.isExon(ann) ) {
if ( rodRefSeq.isCoding(ann) ) b.append(annCoding); // both exon and coding = coding exon sequence
else b.append(annUTR); // exon but not coding = UTR
} else {
if ( ann.isCoding() ) b.append(annIntron);
else b.append(annUnknown);
if ( rodRefSeq.isCoding(ann) ) b.append(annIntron); // not in exon, but within the coding region = intron
else b.append(annUnknown); // we have no idea what this is. this may actually happen when we have a fully non-coding exon...
}
b.append('\t');
Iterator<Transcript> it = ann.getTranscripts().iterator();
b.append(it.next().getGeneName()); // there is at least one transcript in the list, guaranteed
b.append(((Transcript)ann.getRecords().get(0)).getGeneName()); // there is at least one transcript in the list, guaranteed
// while ( it.hasNext() ) { //
// t.getGeneName()
// }