zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Validation of GATKSamRecord in read filters 

Moved the validation of the GATKSamRecord to the MalformedReadFilter with the intent to make the read filter the ultimate validation location for sam records. This way we can opt to filter out malformed reads if we know what we are doing or blow up otherwise.
This commit is contained in:
Mauricio Carneiro 2011-10-21 17:40:43 -04:00
parent 9f867d77ca
commit 102dafdcbc
2 changed files with 24 additions and 6 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

26
public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java
View File

@ -27,7 +27,9 @@ package org.broadinstitute.sting.gatk.filters;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMSequenceRecord;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.exceptions.UserException;
/**
* Filter out malformed reads.
@ -37,14 +39,25 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
*/
public class MalformedReadFilter extends ReadFilter {
private SAMFileHeader header;
@Argument(fullName = "filter_mismatching_base_and_quals", shortName = "filterMBQ", doc = "if a read has mismatching number of bases and base qualities, filter out the read instead of blowing up.", required = false)
boolean filterMismatchingBaseAndQuals = false;
@Override
public void initialize(GenomeAnalysisEngine engine) {
this.header = engine.getSAMFileHeader();
}
public boolean filterOut(SAMRecord read) {
return !checkInvalidAlignmentStart(read) ||
// 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) ||
!checkInvalidAlignmentEnd(read) ||
!checkAlignmentDisagreesWithHeader(this.header,read) ||
!checkCigarDisagreesWithAlignment(read);
@ -108,4 +121,13 @@ public class MalformedReadFilter extends ReadFilter {
return false;
return true;
}
/**
* Check if the read has the same number of bases and base qualities
* @param read the read to validate
* @return true if they have the same number. False otherwise.
*/
private static boolean checkMismatchingBasesAndQuals(SAMRecord read) {
return (read.getReadLength() == read.getBaseQualities().length);
}
}

4
public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
View File

@ -86,10 +86,6 @@ public class GATKSAMRecord extends SAMRecord {
if ( originalQuals != null )
mRecord.setBaseQualities(originalQuals);
}
// sanity check that the lengths of the base and quality strings are equal
if ( getBaseQualities().length != getReadLength() )
throw new UserException.MalformedBAM(this, String.format("Error: the number of base qualities does not match the number of bases in %s.", mRecord.getReadName()));
}
///////////////////////////////////////////////////////////////////////////////