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Fix minor bug introduced in filtration, and cleaned up the artificial sam records so that they use SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX and SAMRecord.NO_ALIGNMENT_START rather than hardcoded -1's. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1296 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-07-22 22:37:41 +00:00
parent cac04a407a
commit 298cc24524
4 changed files with 14 additions and 5 deletions
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6
java/src/org/broadinstitute/sting/utils/sam/ArtificialPatternedSAMIterator.java
View File

@ -113,7 +113,11 @@ public class ArtificialPatternedSAMIterator extends ArtificialSAMIterator {
return false;
} else {
++totalReadCount;
this.next = ArtificialSAMUtils.createArtificialRead(this.header, String.valueOf(totalReadCount), -1, -1, 50);
this.next = ArtificialSAMUtils.createArtificialRead(this.header,
String.valueOf(totalReadCount),
SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX,
SAMRecord.NO_ALIGNMENT_START,
50);
--unmappedRemaining;
return true;
}

6
java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMIterator.java
View File

@ -139,7 +139,11 @@ public class ArtificialSAMIterator implements StingSAMIterator {
return false;
} else {
++totalReadCount;
this.next = ArtificialSAMUtils.createArtificialRead(this.header, String.valueOf(totalReadCount), -1, -1, 50);
this.next = ArtificialSAMUtils.createArtificialRead(this.header,
String.valueOf(totalReadCount),
SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX,
SAMRecord.NO_ALIGNMENT_START,
50);
--unmappedRemaining;
return true;
}

5
java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java
View File

@ -143,7 +143,8 @@ public class ArtificialSAMUtils {
* @return the artificial read
*/
public static SAMRecord createArtificialRead( SAMFileHeader header, String name, int refIndex, int alignmentStart, int length ) {
if (alignmentStart == 0)
if( (refIndex == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX && alignmentStart != SAMRecord.NO_ALIGNMENT_START) ||
(refIndex != SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX && alignmentStart == SAMRecord.NO_ALIGNMENT_START) )
throw new StingException("Invalid alignment start for artificial read, start = " + alignmentStart);
SAMRecord record = new SAMRecord(header);
record.setReadName(name);
@ -153,7 +154,7 @@ public class ArtificialSAMUtils {
elements.add(new CigarElement(length, CigarOperator.characterToEnum('M')));
record.setCigar(new Cigar(elements));
record.setProperPairFlag(false);
if (refIndex == -1) {
if (refIndex == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) {
record.setReadUmappedFlag(true);
}
return record;

2
java/src/org/broadinstitute/sting/utils/sam/SAMReadValidator.java
View File

@ -79,7 +79,7 @@ public class SAMReadValidator {
if( read.getReferenceIndex() == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX && read.getAlignmentStart() != SAMRecord.NO_ALIGNMENT_START )
throw new SAMReadValidationException("Read is aligned to nonexistent contig");
SAMSequenceRecord contigHeader = header.getSequence( read.getReferenceIndex() );
if( read.getReadUnmappedFlag() && read.getAlignmentStart() > contigHeader.getSequenceLength() )
if( !read.getReadUnmappedFlag() && read.getAlignmentStart() > contigHeader.getSequenceLength() )
throw new SAMReadValidationException("Read is aligned to a point after the end of the contig");
}