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Make sure that only reads marked as 'mapped' are filtered based on validity of alignment. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1217 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-07-10 17:44:06 +00:00
parent e01d37024a
commit aa4f60d980
1 changed files with 5 additions and 5 deletions
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10
java/src/org/broadinstitute/sting/utils/sam/SAMReadValidator.java
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@ -66,23 +66,23 @@ public class SAMReadValidator {
* @param read The read to validate.
*/
private static void checkInvalidAlignmentEnd( SAMRecord read ) {
if( read.getAlignmentEnd() != -1 && read.getAlignmentEnd() < read.getAlignmentStart() )
if( !read.getReadUnmappedFlag() && read.getAlignmentEnd() != -1 && read.getAlignmentEnd() < read.getAlignmentStart() )
throw new SAMReadValidationException("Alignment ends prior to its beginning");
}
private static void checkAlignmentDisagreesWithHeader( SAMFileHeader header, SAMRecord read ) {
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");
}
}
}
/**
* Check for inconsistencies between the cigar string and the
* @param read The read to validate.
*/
private static void checkCigarDisagreesWithAlignment( SAMRecord read ) {
if( read.getAlignmentStart() != -1 &&
if( !read.getReadUnmappedFlag() &&
read.getAlignmentStart() != -1 &&
read.getAlignmentStart() != SAMRecord.NO_ALIGNMENT_START &&
read.getAlignmentBlocks().size() == 0 )
throw new SAMReadValidationException("Read has a valid alignment start, but the CIGAR string is empty");