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Changed to accomodate new ROD system 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1671 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-09-21 17:10:56 +00:00
parent d2d1354199
commit fb09835ef8
1 changed files with 6 additions and 8 deletions
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14
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java
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@ -2,10 +2,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.indels;
import net.sf.samtools.*;
import org.broadinstitute.sting.gatk.refdata.RODIterator;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
import org.broadinstitute.sting.gatk.refdata.Transcript;
import org.broadinstitute.sting.gatk.refdata.rodRefSeq;
import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.ReadFilters;
import org.broadinstitute.sting.gatk.filters.Platform454Filter;
@ -70,7 +67,7 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
private java.io.Writer output = null;
private GenomeLoc location = null;
private RODIterator<rodRefSeq> refseqIterator=null;
private SeekableRODIterator<rodRefSeq> refseqIterator=null;
private Set<String> normalReadGroups;
private Set<String> tumorReadGroups ;
@ -412,8 +409,8 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
}
location = GenomeLocParser.setStart(location,pos); location = GenomeLocParser.setStop(location,pos); // retrieve annotation data
rodRefSeq annotation = (refseqIterator == null ? null : refseqIterator.seekForward(location));
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);
@ -513,7 +510,8 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
continue; // too dirty
}
location = GenomeLocParser.setStart(location,pos); location = GenomeLocParser.setStop(location,pos); // retrieve annotation data
rodRefSeq annotation = (refseqIterator == null ? null : refseqIterator.seekForward(location));
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) ) {