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allow clipper to use original quals if requested 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2969 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-03-09 21:50:31 +00:00
parent ee68e38e02
commit bc3761dc16
1 changed files with 21 additions and 4 deletions
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25
java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java
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@ -6,9 +6,7 @@ import net.sf.picard.reference.ReferenceSequenceFile;
import net.sf.picard.reference.ReferenceSequence;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.Pair;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
import java.util.*;
@ -45,6 +43,9 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipper, Cli
@Argument(fullName="read", doc="", required=false)
String onlyDoRead = null;
@Argument(fullName="useOriginalQualities", shortName = "OQ", doc="If set, use the original base quality scores", required=false)
boolean USE_ORIGINAL_QUALS = false;
//@Argument(fullName = "keepCompletelyClipped", shortName = "KCC", doc = "Unfortunately, sometimes a read is completely clipped away but with SOFTCLIP_BASES this results in an invalid CIGAR string. ", required = false)
//boolean keepCompletelyClippedReads = false;
@ -54,6 +55,8 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipper, Cli
@Argument(fullName = "clipRepresentation", shortName = "CR", doc = "How should we actually clip the bases?", required = false)
ClippingRepresentation clippingRepresentation = ClippingRepresentation.WRITE_NS;
private final static String ORIGINAL_QUAL_ATTRIBUTE_TAG = "OQ"; // The tag that holds the original quality scores
/**
* List of sequence that should be clipped from the reads
*/
@ -253,7 +256,21 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipper, Cli
private void clipBadQualityScores(ReadClipper clipper) {
SAMRecord read = clipper.getRead();
int readLen = read.getReadBases().length;
byte[] quals = read.getBaseQualities();
byte[] quals = null;
if ( USE_ORIGINAL_QUALS ) {
final Object attr = read.getAttribute(ORIGINAL_QUAL_ATTRIBUTE_TAG);
if ( attr != null ) {
if ( attr instanceof String ) {
quals = QualityUtils.fastqToPhred((String)attr);
} else {
throw new StingException(String.format("Value encoded by %s in %s isn't a string!", ORIGINAL_QUAL_ATTRIBUTE_TAG, read.getReadName()));
}
}
}
// if we don't want original quals or couldn't find them, use the main quals
if ( quals == null )
quals = read.getBaseQualities();
int clipSum = 0, lastMax = -1, clipPoint = -1; // -1 means no clip