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fixed a bug found by Eric: genotyper would crash in the case of an indel too close to the window end, with the next read mapping sufficiently far away on the ref 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1313 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-07-24 21:00:31 +00:00
parent 2db86b7829
commit 64221907a2
1 changed files with 88 additions and 27 deletions
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115
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java
View File

@ -1,13 +1,16 @@
package org.broadinstitute.sting.playground.gatk.walkers.indels;
import net.sf.picard.sam.SamFileHeaderMerger;
import net.sf.samtools.*;
import org.broadinstitute.sting.gatk.Reads;
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.walkers.ReadWalker;
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.ZeroMappingQualityReadFilter;
import org.broadinstitute.sting.playground.utils.CircularArray;
@ -164,6 +167,53 @@ 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
public Integer map(char[] ref, SAMRecord read) {
@ -357,13 +407,15 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
*/
private void emit(long position, boolean force) {
long stop_at = position; // we will shift to this position instead of passed 'position'
// argument if we did not cover MISMATCH_WIDTH bases around the last indel yet
long move_to = position; // we will shift to position move_to; it's initialized with 'position',
// but it may end up being smaller (delayed shift), if we have not
// covered MISMATCH_WIDTH bases to the right of the last indel yet.
// walk along the coverage window and emit indels up to the position we are trying ot shift the window to
for ( long pos = coverage.getStart() ; pos < Math.min(position,coverage.getStop()+1) ; pos++ ) {
List<IndelVariant> variants = coverage.indelsAt(pos);
if ( variants.size() == 0 ) continue; // no indels
if ( variants.size() == 0 ) continue; // no indels at current position
// if we are here, we got a variant
@ -371,20 +423,27 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
if ( cov < minCoverage ) continue; // low coverage
// System.out.println("indel at "+pos);
// region around the current indel we need to have covered in order to compute mismatch rate:
long left = Math.max( pos-MISMATCH_WIDTH, coverage.getStart() );
long right = pos+MISMATCH_WIDTH;
if ( right > coverage.getStop() ) { // we do not have enough bases in the current window
// in order to assess mismatch rate
if( force ) { // if we were asked to force-shift, then, well, shift anyway
right = coverage.getStop() ;
} else {
// shift to the position prior to the last indel so that we could get all the mismatch counts around it later
stop_at = left;
break;
}
// if right < position we are shifting to, we already have all the coverage within MISMATCH_WINDOW bases around the indel,
// so we can proceed with counting mismatches and emitting the indel
if ( right >= position && ! force) {
// we are not asked to force-shift, and there is more coverage around the current indel that we need to collect
// we are not asked to force-shift, and there's still additional coverage to the right of current indel, so its too early to emit it;
// instead we shift only up to current indel pos - MISMATCH_WIDTH, so that we could keep collecting that coverage
move_to = left;
// System.out.println("right="+right+" requested="+position+" stopped at="+left);
break;
}
if ( right > coverage.getStop() ) right = coverage.getStop(); // if indel is too close to the end of the window but we need to emit anyway
// count mismatches around the current indel, inside specified window (MISMATCH_WIDTH on each side):
int total_mismatches = 0;
for ( long k = left; k <= right ; k++ ) total_mismatches+=coverage.mismatchesAt(k);
@ -404,13 +463,15 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
String annotationString = (refseqIterator == null ? "" : getAnnotationString(annotation));
if ( verbose ) out.println(message + "\t"+ annotationString);
}
}
// else { System.out.println("not a call: count="+p.first.count+" total_count="+p.second+" cov="+cov+
// " minConsensusF="+((double)p.first.count)/p.second+" minF="+((double)p.first.count)/cov); }
// for ( IndelVariant var : variants ) {
// System.out.print("\t"+var.getType()+"\t"+var.getBases()+"\t"+var.getCount());
// }
}
coverage.shift((int)(stop_at - coverage.getStart() ) );
// System.out.println("Shifting to " + move_to+" ("+position+")");
coverage.shift((int)(move_to - coverage.getStart() ) );
}
/** Output somatic indel calls up to the specified position and shift the coverage array(s): after this method is executed
@ -420,7 +481,7 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
*/
private void emit_somatic(long position, boolean force) {
long stop_at = position;
long move_to = position;
for ( long pos = coverage.getStart() ; pos < Math.min(position,coverage.getStop()+1) ; pos++ ) {
@ -440,17 +501,17 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
long left = Math.max( pos-MISMATCH_WIDTH, coverage.getStart() );
long right = pos+MISMATCH_WIDTH;
if ( right > coverage.getStop() ) { // we do not have enough bases in the current window
// in order to assess mismatch rate
if( force ) { // if we were asked to force-shift, then, well, shift anyway
right = coverage.getStop() ;
} else {
// shift to the position prior to the last indel so that we could get all the mismatch counts around it later
stop_at = left;
break;
}
if ( right >= position && ! force) {
// we are not asked to force-shift, and there is more coverage around the current indel that we need to collect
// we are not asked to force-shift, and there's still additional coverage to the right of current indel, so its too early to emit it;
// instead we shift only up to current indel pos - MISMATCH_WIDTH, so that we could keep collecting that coverage
move_to = left;
break;
}
if ( right > coverage.getStop() ) right = coverage.getStop(); // if indel is too close to the end of the window but we need to emit anyway
// count mismatches around the current indel, inside specified window (MISMATCH_WIDTH on each side):
int total_mismatches_normal = 0;
int total_mismatches_tumor = 0;
@ -500,8 +561,8 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
// }
}
coverage.shift((int)(stop_at - coverage.getStart() ) );
normal_coverage.shift((int)(stop_at - normal_coverage.getStart() ) );
coverage.shift((int)(move_to - coverage.getStart() ) );
normal_coverage.shift((int)(move_to - normal_coverage.getStart() ) );
}