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IndelGenotyper now uses GATK::getMergedReadGroupsByReaders() to sort out which read in the merged stream is for normal, and which is for tumor (in --somatic mode, apparently) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1316 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-07-24 23:01:18 +00:00
parent a361e7b342
commit 5eca4c353c
1 changed files with 37 additions and 89 deletions
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120
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java
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@ -1,16 +1,13 @@
package org.broadinstitute.sting.playground.gatk.walkers.indels; package org.broadinstitute.sting.playground.gatk.walkers.indels;
import net.sf.picard.sam.SamFileHeaderMerger;
import net.sf.samtools.*; import net.sf.samtools.*;
import org.broadinstitute.sting.gatk.Reads;
import org.broadinstitute.sting.gatk.refdata.RODIterator; import org.broadinstitute.sting.gatk.refdata.RODIterator;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
import org.broadinstitute.sting.gatk.refdata.Transcript; import org.broadinstitute.sting.gatk.refdata.Transcript;
import org.broadinstitute.sting.gatk.refdata.rodRefSeq; import org.broadinstitute.sting.gatk.refdata.rodRefSeq;
import org.broadinstitute.sting.gatk.walkers.ReadWalker; import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.ReadFilters; import org.broadinstitute.sting.gatk.walkers.ReadFilters;
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource;
import org.broadinstitute.sting.gatk.filters.Platform454Filter; import org.broadinstitute.sting.gatk.filters.Platform454Filter;
import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter; import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
import org.broadinstitute.sting.playground.utils.CircularArray; import org.broadinstitute.sting.playground.utils.CircularArray;
@ -69,8 +66,8 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
private RODIterator<rodRefSeq> refseqIterator=null; private RODIterator<rodRefSeq> refseqIterator=null;
private Set<String> normal_samples = new HashSet<String>(); private Set<String> normalReadGroups;
private Set<String> tumor_samples = new HashSet<String>(); private Set<String> tumorReadGroups ;
private int MISMATCH_WIDTH = 5; // 5 bases on each side of the indel private int MISMATCH_WIDTH = 5; // 5 bases on each side of the indel
private int MISMATCH_CUTOFF = 1000000; private int MISMATCH_CUTOFF = 1000000;
@ -105,6 +102,8 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
location = GenomeLocParser.createGenomeLoc(0,1); location = GenomeLocParser.createGenomeLoc(0,1);
List<Set<String>> readGroupSets = getToolkit().getMergedReadGroupsByReaders();
if ( call_somatic ) { if ( call_somatic ) {
if ( nSams != 2 ) { if ( nSams != 2 ) {
System.out.println("In --somatic mode two input bam files must be specified (normal/tumor)"); System.out.println("In --somatic mode two input bam files must be specified (normal/tumor)");
@ -112,24 +111,35 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
} }
normal_coverage = new RunningCoverage(0,WINDOW_SIZE); normal_coverage = new RunningCoverage(0,WINDOW_SIZE);
// this is an ugly hack: we want to be able to tell what file (tumor/normal sample) each read came from, normalReadGroups = readGroupSets.get(0); // first -I option must specify normal.bam
// but reads do not carry this information! tumorReadGroups = readGroupSets.get(1); // second -I option must specify tumor.bam
// SAMFileReader rn = new SAMFileReader(getToolkit().getArguments().samFiles.get(0));
// for ( SAMReadGroupRecord rec : rn.getFileHeader().getReadGroups() ) {
// normal_samples.add(rec.getSample());
// }
// rn.close();
// rn = new SAMFileReader(getToolkit().getArguments().samFiles.get(1));
// for ( SAMReadGroupRecord rec : rn.getFileHeader().getReadGroups() ) {
// tumor_samples.add(rec.getSample());
// }
// rn.close();
} else { } else {
if ( nSams != 1 ) System.out.println("WARNING: multiple input files specified. \n"+ if ( nSams != 1 ) System.out.println("WARNING: multiple input files specified. \n"+
"WARNING: Without --somatic option they will be merged and processed as a single sample"); "WARNING: Without --somatic option they will be merged and processed as a single sample");
} }
/*
List<Set<String>> sample_sets = getToolkit().getSamplesByReaders();
for ( int i = 0 ; i < sample_sets.size() ; i++ ) {
System.out.print("Reader "+i);
for ( String s : sample_sets.get(i) ) System.out.print(" " + s);
System.out.println();
}
List<Set<String>> lib_sets = getToolkit().getLibrariesByReaders();
for ( int i = 0 ; i < lib_sets.size() ; i++ ) {
System.out.print("Reader "+i);
for ( String s : lib_sets.get(i) ) System.out.print(" " + s);
System.out.println();
}
*/
/*
for ( int i = 0 ; i < readGroupSets.size() ; i++ ) {
System.out.print("Reader "+i);
for ( String s : readGroupSets.get(i) ) System.out.print(" " + s);
System.out.println();
}
assignReadGroups1();
*/
try { try {
output = new java.io.FileWriter(bed_file); output = new java.io.FileWriter(bed_file);
} catch (IOException e) { } catch (IOException e) {
@ -137,6 +147,7 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
} }
} }
/*
void assignReadGroups(final SAMFileHeader mergedHeader) { void assignReadGroups(final SAMFileHeader mergedHeader) {
Set<String> normal = new HashSet<String>(); // list normal samples here Set<String> normal = new HashSet<String>(); // list normal samples here
@ -167,74 +178,19 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
} }
*/
void assignReadGroups1(final SAMFileHeader mergedHeader) {
SAMDataSource d = getToolkit().getDataSource();
Reads reads = d.getReadsInfo();
System.out.println(reads.getReadsFiles().size() + " input files");
System.out.println(d.getHeaderMerger().getReaders().size() +" readers instantiated");
for ( SAMFileReader r : d.getHeaderMerger().getReaders() ) {
System.out.print("----------\nread groups:");
for ( SAMReadGroupRecord g : r.getFileHeader().getReadGroups() ) {
System.out.print(" "+g.getReadGroupId()+ " ("+g.getSample()+":"+g.getLibrary()+")");
}
}
System.exit(1);
Set<String> normal = new HashSet<String>(); // list normal samples here
Set<String> tumor = new HashSet<String>(); // list tumor samples here
SAMFileReader rn = new SAMFileReader(getToolkit().getArguments().samFiles.get(0));
for ( SAMReadGroupRecord rec : rn.getFileHeader().getReadGroups() ) {
normal.add(new String(rec.getSample()));
}
rn.close();
rn = new SAMFileReader(getToolkit().getArguments().samFiles.get(1));
for ( SAMReadGroupRecord rec : rn.getFileHeader().getReadGroups() ) {
tumor.add(new String(rec.getSample()));
}
rn.close();
// now we know what samples are normal, and what are tumor; let's assign dynamic read groups we get in merged header:
for ( SAMReadGroupRecord mr : mergedHeader.getReadGroups() ) {
if ( normal.contains(mr.getSample() ) ) {
normal_samples.add( new String(mr.getReadGroupId()) );
System.out.println("Read group "+ mr.getReadGroupId() + "--> Sample "+ mr.getSample() + " (normal)");
} else if ( tumor.contains(mr.getSample() ) ) {
tumor_samples.add( new String(mr.getReadGroupId()) );
System.out.println("Read group "+ mr.getReadGroupId() + "--> Sample "+ mr.getSample() + " (tumor)");
} else throw new StingException("Unrecognized sample "+mr.getSample() +" in merged SAM stream");
}
System.out.println();
}
@Override @Override
public Integer map(char[] ref, SAMRecord read) { public Integer map(char[] ref, SAMRecord read) {
// if ( read.getReadUnmappedFlag() && read.getReferenceIndex() == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX &&
// read.getAlignmentStart() == SAMRecord.NO_ALIGNMENT_START ) {
// System.out.println("I think I reached unmapped reads at the end of the file(s) and I am done...");
// return 0;
// }
// if ( read.getAlignmentStart() < 112337549 && read.getAlignmentEnd() > 112337550 ) {
// System.out.print("adding "+read.getReadString()+" "+read.getCigarString());
// }
if ( read.getReadUnmappedFlag() || if ( read.getReadUnmappedFlag() ||
read.getDuplicateReadFlag() || read.getDuplicateReadFlag() ||
read.getNotPrimaryAlignmentFlag() || read.getNotPrimaryAlignmentFlag() ||
read.getMappingQuality() == 0 ) { read.getMappingQuality() == 0 ) {
// System.out.println(" ignored");
return 0; // we do not need those reads! return 0; // we do not need those reads!
} }
// System.out.print(" added");
if ( read.getReferenceIndex() != currentContigIndex ) { if ( read.getReferenceIndex() != currentContigIndex ) {
// we just jumped onto a new contig // we just jumped onto a new contig
@ -249,7 +205,6 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
refName = new String(read.getReferenceName()); refName = new String(read.getReferenceName());
location = GenomeLocParser.setContig(location,refName); location = GenomeLocParser.setContig(location,refName);
// location.setContigIndex(read.getReferenceIndex());
coverage.clear(); // reset coverage window; this will also set reference position to 0 coverage.clear(); // reset coverage window; this will also set reference position to 0
if ( call_somatic) normal_coverage.clear(); if ( call_somatic) normal_coverage.clear();
@ -306,19 +261,12 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
if ( call_somatic ) { if ( call_somatic ) {
// this is a hack. currently we can get access to the merged header only through the read,
// so below we figure out which of the reassigned read groups in the merged stream are normal
// and which are tumor, and we make sure we do it only once:
if ( normal_samples.size() == 0 ) assignReadGroups(read.getHeader());
String rg = (String)read.getAttribute("RG"); String rg = (String)read.getAttribute("RG");
if ( rg == null ) throw new StingException("Read "+read.getReadName()+" has no read group in merged stream"); if ( rg == null ) throw new StingException("Read "+read.getReadName()+" has no read group in merged stream");
if ( normal_samples.contains(rg) ) { if ( normalReadGroups.contains(rg) ) {
// System.out.println(" TO NORMAL");
normal_coverage.add(read,ref); normal_coverage.add(read,ref);
} else if ( tumor_samples.contains(rg) ) { } else if ( tumorReadGroups.contains(rg) ) {
// System.out.println(" TO TUMOR");
coverage.add(read,ref); coverage.add(read,ref);
} else { } else {
throw new StingException("Unrecognized read group in merged stream: "+rg); throw new StingException("Unrecognized read group in merged stream: "+rg);
@ -653,7 +601,7 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
public String getSamples() { public String getSamples() {
StringBuffer sb = new StringBuffer(); StringBuffer sb = new StringBuffer();
Iterator i = samples.iterator(); Iterator<String> i = samples.iterator();
while ( i.hasNext() ) { while ( i.hasNext() ) {
sb.append(i.next()); sb.append(i.next());
if ( i.hasNext() ) if ( i.hasNext() )