now has two modes: one sample - just call indel sites; two samples - call somatic-looking variants only. Still uses heuristic count-based cutoffs, cutoffs are hardcoded and are pretty conservative...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@967 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache
parent
5451bbfd5a
commit
06e5a765f8
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@ -1,25 +1,77 @@
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package org.broadinstitute.sting.playground.gatk.walkers.indels;
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import java.io.IOException;
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import java.util.ArrayList;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Set;
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import net.sf.samtools.Cigar;
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import net.sf.samtools.CigarElement;
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import net.sf.samtools.SAMFileReader;
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import net.sf.samtools.SAMReadGroupRecord;
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import net.sf.samtools.SAMRecord;
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import org.broadinstitute.sting.gatk.walkers.ReadWalker;
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import org.broadinstitute.sting.playground.utils.CircularArray;
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import org.broadinstitute.sting.utils.StingException;
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import org.broadinstitute.sting.utils.cmdLine.Argument;
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public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
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@Argument(fullName="bed", shortName="bed", doc="BED output file name", required=true)
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public java.io.File bed_file;
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@Argument(fullName="somatic", shortName="somatic",
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doc="Perform somatic calls; two input alignment files must be specified", required=false)
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public boolean call_somatic = false;
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private static int WINDOW_SIZE = 200;
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private RunningCoverage coverage;
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private RunningCoverage normal_coverage; // when performing somatic calls, we will be using this one for normal, and 'coverage' for tumor
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private int currentContigIndex = -1;
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private String refName = null;
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private java.io.Writer output = null;
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private Set<String> normal_samples = new HashSet<String>();
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private Set<String> tumor_samples = new HashSet<String>();
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@Override
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public void initialize() {
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coverage = new RunningCoverage(0,100);
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coverage = new RunningCoverage(0,WINDOW_SIZE);
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int nSams = getToolkit().getArguments().samFiles.size();
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if ( call_somatic ) {
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if ( nSams != 2 ) {
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System.out.println("In --somatic mode two input bam files must be specified (normal/tumor)");
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System.exit(1);
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}
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normal_coverage = new RunningCoverage(0,WINDOW_SIZE);
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// this is an ugly hack: we want to be able to tell what file (tumor/normal sample) each read came from,
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// but reads do not carry this information!
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SAMFileReader rn = new SAMFileReader(getToolkit().getArguments().samFiles.get(0));
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for ( SAMReadGroupRecord rec : rn.getFileHeader().getReadGroups() ) {
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normal_samples.add(rec.getSample());
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}
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rn.close();
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rn = new SAMFileReader(getToolkit().getArguments().samFiles.get(1));
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for ( SAMReadGroupRecord rec : rn.getFileHeader().getReadGroups() ) {
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tumor_samples.add(rec.getSample());
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}
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rn.close();
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} else {
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if ( nSams != 1 ) System.out.println("WARNING: multiple input files specified. \n"+
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"WARNING: Without --somatic option they will be merged and processed as a single sample");
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}
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try {
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output = new java.io.FileWriter(bed_file);
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} catch (IOException e) {
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throw new StingException("Failed to open file for writing BED output");
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}
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}
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@Override
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@ -30,13 +82,19 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
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read.getNotPrimaryAlignmentFlag() ||
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read.getMappingQuality() == 0 ) return 0; // we do not need those reads!
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if ( read.getReferenceIndex() != currentContigIndex ) {
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if ( read.getReferenceIndex() != currentContigIndex ) {
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// we just jumped onto a new contig
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if ( read.getReferenceIndex() < currentContigIndex ) // paranoidal
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throw new StingException("Read "+read.getReadName()+": contig is out of order");
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if ( call_somatic) emit_somatic(1000000000); // print remaining indels from the previous contig (if any);
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else emit(1000000000);
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currentContigIndex = read.getReferenceIndex();
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refName = new String(read.getReferenceName());
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coverage.clear(); // reset coverage window; this will also set reference position to 0
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if ( call_somatic) normal_coverage.clear();
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}
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if ( read.getAlignmentStart() < coverage.getStart() ) {
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@ -46,30 +104,164 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
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// reads are sorted; we are not going to see any more coverage or new indels prior
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// to current read's start position!
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for ( long pos = coverage.getStart() ; pos < Math.min(read.getAlignmentStart(),coverage.getStop()+1) ; pos++ ) {
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List<IndelVariant> variants = coverage.indelsAt(pos);
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if ( variants.size() == 0 ) continue;
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System.out.print(read.getReferenceName()+"\t"+pos+"\t"+coverage.coverageAt(pos));
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for ( IndelVariant var : variants ) {
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System.out.print("\t"+var.getType()+"\t"+var.getBases()+"\t"+var.getCount());
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}
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System.out.println();
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}
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coverage.shift((int)(read.getAlignmentStart() - coverage.getStart() ) );
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if ( call_somatic ) emit_somatic( read.getAlignmentStart() );
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else emit( read.getAlignmentStart() );
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if ( read.getAlignmentEnd() > coverage.getStop()) {
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// should never happen
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throw new StingException("Read "+read.getReadName()+": out of coverage window bounds");
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throw new StingException("Read "+read.getReadName()+": out of coverage window bounds.\n"+
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"Read length="+read.getReadLength()+"; cigar="+read.getCigarString()+"; start="+
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read.getAlignmentStart()+"; end="+read.getAlignmentEnd()+"; window start="+coverage.getStart()+
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"; window end="+coverage.getStop());
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}
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coverage.add(read,ref);
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if ( call_somatic ) {
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String rg = (String)read.getAttribute("RG");
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String sample = read.getHeader().getReadGroup(rg).getSample();
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if ( normal_samples.contains(sample) ) {
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normal_coverage.add(read,ref);
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} else if ( tumor_samples.contains(sample) ) {
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coverage.add(read,ref);
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} else {
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throw new StingException("Unrecognized sample: "+sample);
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}
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} else {
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coverage.add(read, ref);
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}
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return 1;
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}
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/** Output indel calls up to the specified position and shift the coverage array(s): after this method is executed
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* first elements of the coverage arrays map onto 'position'
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*
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* @param position
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*/
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private void emit(long position) {
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for ( long pos = coverage.getStart() ; pos < Math.min(position,coverage.getStop()+1) ; pos++ ) {
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List<IndelVariant> variants = coverage.indelsAt(pos);
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if ( variants.size() == 0 ) continue; // no indels
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int cov = coverage.coverageAt(pos);
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if ( cov < 6 ) continue; // low coverage
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int total_variant_count = 0;
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int max_variant_count = 0;
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String indelString = null;
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int event_length = 0; // length of the event on the reference
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for ( IndelVariant var : variants ) {
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int cnt = var.getCount();
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total_variant_count +=cnt;
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if ( cnt > max_variant_count ) {
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max_variant_count = cnt;
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indelString = var.getBases();
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event_length = var.lengthOnRef();
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}
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}
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if ( (double)total_variant_count > 0.3*cov && (double) max_variant_count > 0.7*total_variant_count ) {
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try {
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output.write(refName+"\t"+(pos-1)+"\t"+(event_length > 0 ? pos-1+event_length : pos-1)+
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"\t"+(event_length>0? "-":"+")+indelString +":"+total_variant_count+"/"+cov+"\n");
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} catch (IOException e) {
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System.out.println(e.getMessage());
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e.printStackTrace();
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throw new StingException("Error encountered while writing into output BED file");
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}
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}
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// for ( IndelVariant var : variants ) {
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// System.out.print("\t"+var.getType()+"\t"+var.getBases()+"\t"+var.getCount());
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// }
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}
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coverage.shift((int)(position - coverage.getStart() ) );
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}
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/** Output somatic indel calls up to the specified position and shift the coverage array(s): after this method is executed
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* first elements of the coverage arrays map onto 'position'
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*
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* @param position
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*/
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private void emit_somatic(long position) {
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for ( long pos = coverage.getStart() ; pos < Math.min(position,coverage.getStop()+1) ; pos++ ) {
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List<IndelVariant> tumor_variants = coverage.indelsAt(pos);
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List<IndelVariant> normal_variants = normal_coverage.indelsAt(pos);
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if ( tumor_variants.size() == 0 ) continue; // no indels in tumor
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int tumor_cov = coverage.coverageAt(pos);
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int normal_cov = normal_coverage.coverageAt(pos);
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if ( tumor_cov < 6 ) continue; // low coverage
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if ( normal_cov < 4 ) continue; // low coverage
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int total_variant_count_tumor = 0;
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int max_variant_count_tumor = 0;
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String indelStringTumor = null;
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int event_length_tumor = 0; // length of the event on the reference
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for ( IndelVariant var : tumor_variants ) {
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int cnt = var.getCount();
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total_variant_count_tumor +=cnt;
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if ( cnt > max_variant_count_tumor ) {
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max_variant_count_tumor = cnt;
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indelStringTumor = var.getBases();
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event_length_tumor = var.lengthOnRef();
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}
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}
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if ( (double)total_variant_count_tumor > 0.3*tumor_cov && (double) max_variant_count_tumor > 0.7*total_variant_count_tumor ) {
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System.out.println(refName+"\t"+(pos-1)+"\t"+(event_length_tumor > 0 ? pos-1+event_length_tumor : pos-1)+
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"\t"+(event_length_tumor >0? "-":"+")+indelStringTumor +":"+total_variant_count_tumor+"/"+tumor_cov);
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if ( normal_variants.size() == 0 ) {
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try {
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output.write(refName+"\t"+(pos-1)+"\t"+(event_length_tumor > 0 ? pos-1+event_length_tumor : pos-1)+
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"\t"+(event_length_tumor >0? "-":"+")+indelStringTumor +":"+total_variant_count_tumor+"/"+tumor_cov+"\n");
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} catch (IOException e) {
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System.out.println(e.getMessage());
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e.printStackTrace();
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throw new StingException("Error encountered while writing into output BED file");
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}
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System.out.println("INDICATION FOR SOMATIC\n---------------------------\n");
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} else {
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System.out.println("INDICATION FOR GERMLINE\n---------------------------\n");
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}
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}
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// for ( IndelVariant var : variants ) {
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// System.out.print("\t"+var.getType()+"\t"+var.getBases()+"\t"+var.getCount());
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// }
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}
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coverage.shift((int)(position - coverage.getStart() ) );
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normal_coverage.shift((int)(position - normal_coverage.getStart() ) );
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}
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@Override
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public void onTraversalDone(Integer result) {
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emit(1000000000); // emit everything we might have left
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try {
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output.close();
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} catch (IOException e) {
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System.out.println("Failed to close output BED file gracefully, data may be lost");
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e.printStackTrace();
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}
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super.onTraversalDone(result);
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}
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@Override
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public Integer reduce(Integer value, Integer sum) {
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sum += value;
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@ -99,6 +291,15 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
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count += i;
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}
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/** Returns length of the event on the reference (number of deleted bases
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* for deletions, -1 for insertions.
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* @return
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*/
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public int lengthOnRef() {
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if ( type == Type.D ) return bases.length();
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else return -1;
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}
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public void increment() { count+=1; }
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public int getCount() { return count; }
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@ -235,8 +436,8 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
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if ( type == null ) continue; // element was not an indel, go grab next element...
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// we got an indel if we are here...
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if ( i == 0 ) System.out.println("WARNING: Indel at the start of the read "+r.getReadName());
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if ( i == nCigarElems - 1) System.out.println("WARNING: Indel at the end of the read "+r.getReadName());
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if ( i == 0 ) logger.warn("Indel at the start of the read "+r.getReadName());
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if ( i == nCigarElems - 1) logger.warn("Indel at the end of the read "+r.getReadName());
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updateCount(indelPosition, type, bases);
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}
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