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Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Mark DePristo 2011-11-10 16:05:43 -05:00
parent 153e52ffed 060c7ce8ae
commit bb7bf74aa8
1 changed files with 18 additions and 9 deletions
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27
public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java
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@ -50,19 +50,20 @@ public class MalformedReadFilter extends ReadFilter {
public boolean filterOut(SAMRecord read) { public boolean filterOut(SAMRecord read) {
// slowly changing the behavior to blow up first and filtering out if a parameter is explicitly provided // slowly changing the behavior to blow up first and filtering out if a parameter is explicitly provided
if (!checkMismatchingBasesAndQuals(read)) {
if (!filterMismatchingBaseAndQuals)
throw new UserException.MalformedBAM(read, "BAM file has a read with mismatching number of bases and base qualities. Offender: " + read.getReadName() +" [" + read.getReadLength() + " bases] [" +read.getBaseQualities().length +"] quals");
else
return true;
}
return !checkInvalidAlignmentStart(read) || return !checkInvalidAlignmentStart(read) ||
!checkInvalidAlignmentEnd(read) || !checkInvalidAlignmentEnd(read) ||
!checkAlignmentDisagreesWithHeader(this.header,read) || !checkAlignmentDisagreesWithHeader(this.header,read) ||
!checkHasReadGroup(read) ||
!checkMismatchingBasesAndQuals(read, filterMismatchingBaseAndQuals) ||
!checkCigarDisagreesWithAlignment(read); !checkCigarDisagreesWithAlignment(read);
} }
private static boolean checkHasReadGroup(SAMRecord read) {
if ( read.getReadGroup() == null )
throw new UserException.ReadMissingReadGroup(read);
return true;
}
/** /**
* Check for the case in which the alignment start is inconsistent with the read unmapped flag. * Check for the case in which the alignment start is inconsistent with the read unmapped flag.
* @param read The read to validate. * @param read The read to validate.
@ -127,7 +128,15 @@ public class MalformedReadFilter extends ReadFilter {
* @param read the read to validate * @param read the read to validate
* @return true if they have the same number. False otherwise. * @return true if they have the same number. False otherwise.
*/ */
private static boolean checkMismatchingBasesAndQuals(SAMRecord read) { private static boolean checkMismatchingBasesAndQuals(SAMRecord read, boolean filterMismatchingBaseAndQuals) {
return (read.getReadLength() == read.getBaseQualities().length); boolean result;
if (read.getReadLength() == read.getBaseQualities().length)
result = true;
else if (filterMismatchingBaseAndQuals)
result = false;
else
throw new UserException.MalformedBAM(read, String.format("BAM file has a read with mismatching number of bases and base qualities. Offender: %s [%d bases] [%d quals]", read.getReadName(), read.getReadLength(), read.getBaseQualities().length));
return result;
} }
} }