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Remove the adaptor sequence clipping read filter because it is dangerous (it breaks LocusIteratorByState). We'll bring it back to life when ReadTransformers are created. Instead, have the utility code return a new clipped SAMRecord (necessary so that we don't break SNP calling in UG when the indel caller tries to hard-clip the reads). 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5629 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-04-13 18:47:47 +00:00
parent 5849e112e1
commit fa6468d167
2 changed files with 40 additions and 59 deletions
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44
java/src/org/broadinstitute/sting/gatk/filters/AdaptorSequenceFilter.java
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@ -1,44 +0,0 @@
/*
* Copyright (c) 2009 The Broad Institute
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
/**
* This class doesn't actually filter out reads (it's really a ReadTransformer): it hard-clips the
* reads to remove the adaptor sequences from them.
*
* @author ebanks, depristo
* @version 0.1
*/
public class AdaptorSequenceFilter implements SamRecordFilter {
public boolean filterOut(final SAMRecord rec) {
return ReadUtils.hardClipAdaptorSequence(rec);
}
}

55
java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
View File

@ -176,27 +176,41 @@ public class ReadUtils {
return new Pair<Integer, Integer>(adaptorStart, adaptorEnd);
}
// return true if the read needs to be completely clipped
public static boolean hardClipAdaptorSequence(final SAMRecord rec, int adaptorLength) {
/**
*
* @param rec original SAM record
* @param adaptorLength length of adaptor sequence
* @return a new read with adaptor sequence hard-clipped out or null if read is fully clipped
*/
public static SAMRecord hardClipAdaptorSequence(final SAMRecord rec, int adaptorLength) {
Pair<Integer, Integer> adaptorBoundaries = getAdaptorBoundaries(rec, adaptorLength);
SAMRecord result = rec;
if ( adaptorBoundaries != null ) {
if ( rec.getReadNegativeStrandFlag() && adaptorBoundaries.second >= rec.getAlignmentStart() && adaptorBoundaries.first < rec.getAlignmentEnd() )
return hardClipStartOfRead(rec, adaptorBoundaries.second);
result = hardClipStartOfRead(rec, adaptorBoundaries.second);
else if ( !rec.getReadNegativeStrandFlag() && adaptorBoundaries.first <= rec.getAlignmentEnd() )
return hardClipEndOfRead(rec, adaptorBoundaries.first);
result = hardClipEndOfRead(rec, adaptorBoundaries.first);
}
return false;
return result;
}
// return true if the read needs to be completely clipped
private static boolean hardClipStartOfRead(SAMRecord rec, int stopPosition) {
private static SAMRecord hardClipStartOfRead(SAMRecord oldRec, int stopPosition) {
if ( stopPosition >= rec.getAlignmentEnd() ) {
if ( stopPosition >= oldRec.getAlignmentEnd() ) {
// BAM representation issue -- we can't clip away all bases in a read, just leave it alone and let the filter deal with it
//System.out.printf("Entire read needs to be clipped: %50s %n", rec.getReadName());
return true;
return null;
}
SAMRecord rec;
try {
rec = (SAMRecord)oldRec.clone();
} catch (Exception e) {
return null;
}
//System.out.printf("Clipping start of read: %50s start=%d adaptorEnd=%d isize=%d %n",
@ -261,16 +275,22 @@ public class ReadUtils {
// adjust the start accordingly
rec.setAlignmentStart(stopPosition + 1);
return false;
return rec;
}
// return true if the read needs to be completely clipped
private static boolean hardClipEndOfRead(SAMRecord rec, int startPosition) {
private static SAMRecord hardClipEndOfRead(SAMRecord oldRec, int startPosition) {
if ( startPosition <= rec.getAlignmentStart() ) {
if ( startPosition <= oldRec.getAlignmentStart() ) {
// BAM representation issue -- we can't clip away all bases in a read, just leave it alone and let the filter deal with it
//System.out.printf("Entire read needs to be clipped: %50s %n", rec.getReadName());
return true;
return null;
}
SAMRecord rec;
try {
rec = (SAMRecord)oldRec.clone();
} catch (Exception e) {
return null;
}
//System.out.printf("Clipping end of read: %50s adaptorStart=%d end=%d isize=%d %n",
@ -341,12 +361,17 @@ public class ReadUtils {
// adjust the stop accordingly
// rec.setAlignmentEnd(startPosition - 1);
return false;
return rec;
}
private static int DEFAULT_ADAPTOR_SIZE = 100;
public static boolean hardClipAdaptorSequence(final SAMRecord rec) {
/**
*
* @param rec original SAM record
* @return a new read with adaptor sequence hard-clipped out or null if read is fully clipped
*/
public static SAMRecord hardClipAdaptorSequence(final SAMRecord rec) {
return hardClipAdaptorSequence(rec, DEFAULT_ADAPTOR_SIZE);
}