zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

added filtering out indels with large levels of noise (mismatches) remaining in the close proximity; also a bug in recording deletion coordinates is fixed 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1014 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-06-15 21:13:28 +00:00
parent a6477df6d1
commit 2259dc3a8f
1 changed files with 105 additions and 20 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

125
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java
View File

@ -18,6 +18,7 @@ import org.broadinstitute.sting.gatk.refdata.RODIterator;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
import org.broadinstitute.sting.gatk.refdata.rodRefSeq;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.playground.indels.AlignmentUtils;
import org.broadinstitute.sting.playground.utils.CircularArray;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.StingException;
@ -59,6 +60,10 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
private Set<String> normal_samples = new HashSet<String>();
private Set<String> tumor_samples = new HashSet<String>();
private int MISMATCH_WIDTH = 5; // 5 bases on each side of the indel
private int MISMATCH_CUTOFF = 1000000;
private double AV_MISMATCHES_PER_READ = 1.5;
private static String annGenomic = "GENOMIC";
private static String annIntron = "INTRON";
@ -162,8 +167,8 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
if ( read.getReferenceIndex() < currentContigIndex ) // paranoidal
throw new StingException("Read "+read.getReadName()+": contig is out of order");
if ( call_somatic) emit_somatic(1000000000); // print remaining indels from the previous contig (if any);
else emit(1000000000);
if ( call_somatic) emit_somatic(1000000000, true); // print remaining indels from the previous contig (if any);
else emit(1000000000,true);
currentContigIndex = read.getReferenceIndex();
refName = new String(read.getReferenceName());
location.setContig(refName);
@ -199,8 +204,8 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
// Clearly, we assume here that window is large enough to accomodate any single read, so simply shifting
// the window to the read's start will ensure that the read fits...
if ( call_somatic ) emit_somatic( read.getAlignmentStart() );
else emit( read.getAlignmentStart() );
if ( call_somatic ) emit_somatic( read.getAlignmentStart(), false );
else emit( read.getAlignmentStart(), false );
if ( read.getAlignmentEnd() > coverage.getStop()) {
// ooops, looks like the read does not fit into the current window!!
@ -240,17 +245,46 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
*
* @param position
*/
private void emit(long position) {
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
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 we are here, we got a variant
int cov = coverage.coverageAt(pos);
if ( cov < minCoverage ) continue; // low coverage
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;
}
}
// 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);
if ( total_mismatches > MISMATCH_CUTOFF || total_mismatches > ((double)cov)*AV_MISMATCHES_PER_READ) {
System.out.println(refName+"\t"+(pos-1)+"\t"+
"\tTOO DIRTY\t"+total_mismatches);
continue; // too dirty
}
location.setStart(pos); location.setStop(pos); // retrieve annotation data
rodRefSeq annotation = refseqIterator.seekForward(location);
@ -289,7 +323,7 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
// }
}
coverage.shift((int)(position - coverage.getStart() ) );
coverage.shift((int)(stop_at - coverage.getStart() ) );
}
/** Output somatic indel calls up to the specified position and shift the coverage array(s): after this method is executed
@ -297,7 +331,9 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
*
* @param position
*/
private void emit_somatic(long position) {
private void emit_somatic(long position, boolean force) {
long stop_at = position;
for ( long pos = coverage.getStart() ; pos < Math.min(position,coverage.getStop()+1) ; pos++ ) {
@ -314,6 +350,38 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
if ( tumor_cov < minCoverage ) continue; // low coverage
if ( normal_cov < minNormalCoverage ) continue; // low coverage
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;
}
}
// count mismatches around the current indel, inside specified window (MISMATCH_WIDTH on each side):
int total_mismatches_normal = 0;
int total_mismatches_tumor = 0;
for ( long k = left; k <= right ; k++ ) {
total_mismatches_tumor+=coverage.mismatchesAt(k);
total_mismatches_normal+=normal_coverage.mismatchesAt(k);
}
if ( total_mismatches_normal > MISMATCH_CUTOFF || total_mismatches_normal > ((double)normal_cov)*AV_MISMATCHES_PER_READ) {
System.out.println(refName+"\t"+(pos-1)+"\t"+
"\tNORMAL TOO DIRTY\t"+total_mismatches_normal);
continue; // too dirty
}
if ( total_mismatches_tumor > MISMATCH_CUTOFF || total_mismatches_tumor > ((double)tumor_cov)*AV_MISMATCHES_PER_READ) {
System.out.println(refName+"\t"+(pos-1)+"\t"+
"\tTUMOR TOO DIRTY\t"+total_mismatches_tumor);
continue; // too dirty
}
location.setStart(pos); location.setStop(pos); // retrieve annotation data
rodRefSeq annotation = refseqIterator.seekForward(location);
@ -336,7 +404,13 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
if ( (double)total_variant_count_tumor > minFraction * tumor_cov && (double) max_variant_count_tumor > minConsensusFraction*total_variant_count_tumor ) {
String annotationString = getAnnotationString(annotation);
/*
int leftpos = pos-1;
int rightpos = pos-1;
if ( event_length_tumor > 0 ) {
leftpos -= event_length;
}
*/
String message = refName+"\t"+(pos-1)+"\t"+(event_length_tumor > 0 ? pos-1+event_length_tumor : pos-1)+
"\t"+(event_length_tumor >0? "-":"+")+indelStringTumor +":"+total_variant_count_tumor+"/"+tumor_cov;
if ( normal_variants.size() == 0 ) {
@ -381,7 +455,8 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
@Override
public void onTraversalDone(Integer result) {
emit(1000000000); // emit everything we might have left
if ( call_somatic ) emit_somatic(1000000000, true);
else emit(1000000000,true); // emit everything we might have left
try {
output.close();
} catch (IOException e) {
@ -458,6 +533,7 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
private CircularArray.Int coverageWindow;
private CircularArray< List< IndelVariant > > indels;
private CircularArray.Int mismatches;
private static List<IndelVariant> emptyIndelList;
@ -469,6 +545,7 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
this.start = start;
coverageWindow = new CircularArray.Int(length);
indels = new CircularArray< List<IndelVariant> >(length);
mismatches = new CircularArray.Int(length);
}
/** Returns 1-based reference start position of the interval this object keeps coverage for.
@ -492,6 +569,8 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
return coverageWindow.get( (int)( refPos - start ) );
}
public int mismatchesAt(final long refPos) { return mismatches.get((int)(refPos-start)); }
public List<IndelVariant> indelsAt( final long refPos ) {
List<IndelVariant> l = indels.get((int)( refPos - start ));
if ( l == null ) return emptyIndelList;
@ -507,11 +586,13 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
public void add(SAMRecord r, char [] ref) {
final long rStart = r.getAlignmentStart();
final long rStop = r.getAlignmentEnd();
final String readBases = r.getReadString().toUpperCase();
int localStart = (int)( rStart - start ); // start of the alignment wrt start of the current window
try {
for ( int k = localStart; k <= (int)(rStop-start) ; k++ ) coverageWindow.increment(k, 1);
for ( int k = localStart; k <= (int)(rStop-start) ; k++ ) coverageWindow.increment(k, 1);
} catch ( IndexOutOfBoundsException e) { // replace the message and re-throw:
throw new IndexOutOfBoundsException("Current coverage window: "+getStart()+"-"+getStop()+
"; illegal attempt to add read spanning "+rStart+"-"+rStop);
@ -528,22 +609,20 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
int posOnRead = 0;
int posOnRef = 0; // the chunk of reference ref[] that we have access to is aligned with the read:
// its start on the actual full reference contig is r.getAlignmentStart()
// int mm=0;
for ( int i = 0 ; i < nCigarElems ; i++ ) {
final CigarElement ce = c.getCigarElement(i);
IndelVariant.Type type = null;
String bases = null;
int eventPosition = posOnRef;
int indelPosition = 0; // indel position in our coverage window (i.e. relative to getStart()).
// note that here we assign indels to the first deleted base or to the first
// base after insertion
switch(ce.getOperator()) {
case I:
type = IndelVariant.Type.I;
bases = r.getReadString().substring(posOnRead,posOnRead+ce.getLength());
indelPosition = localStart + posOnRef ;
bases = readBases.substring(posOnRead,posOnRead+ce.getLength());
// will increment position on the read below, there's no 'break' statement yet...
case H:
case S:
@ -555,12 +634,13 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
case D:
type = IndelVariant.Type.D;
bases = new String( ref, posOnRef, ce.getLength() );
indelPosition = localStart + posOnRef ;
posOnRef += ce.getLength();
break;
case M:
posOnRef += ce.getLength();
posOnRead += ce.getLength();
case M: for ( int k = 0; k < ce.getLength(); k++, posOnRef++, posOnRead++ ) {
if ( readBases.charAt(posOnRead) != Character.toUpperCase(ref[posOnRef]) ) { // mismatch!
mismatches.increment(localStart+posOnRef, 1); //mm++;
}
}
break; // advance along the gapless block in the alignment
default :
throw new IllegalArgumentException("Unexpected operator in cigar string: "+ce.getOperator());
@ -573,7 +653,9 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
if ( i == nCigarElems - 1) logger.warn("Indel at the end of the read "+r.getReadName());
try {
updateCount(indelPosition, type, bases);
// note that here we will be assigning indels to the first deleted base or to the first
// base after insertion, not to the last base before the event!
updateCount(localStart+eventPosition, type, bases);
} catch (IndexOutOfBoundsException e) {
System.out.println("Read "+r.getReadName()+": out of coverage window bounds.Probably window is too small.\n"+
"Read length="+r.getReadLength()+"; cigar="+r.getCigarString()+"; start="+
@ -583,6 +665,8 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
}
}
// System.out.println(r.getReadName()+"\t"+(r.getReadNegativeStrandFlag()?"RC":"FW")+"\t"+r.getCigarString()+"\t"+mm);
// System.out.println(AlignmentUtils.alignmentToString(r.getCigar(), readBases, new String(ref), 0));
}
@ -633,6 +717,7 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
start += offset;
coverageWindow.shiftData(offset);
indels.shiftData(offset);
mismatches.shiftData(offset);
}
}