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Clarified that this also filters supplementary alignments.
This commit is contained in:
sooheelee 2016-06-23 16:20:00 -04:00 committed by GitHub
parent 4eff18a470
commit 6fe80d53d0
1 changed files with 3 additions and 3 deletions
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6
public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/NotPrimaryAlignmentFilter.java
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@ -28,9 +28,9 @@ package org.broadinstitute.gatk.engine.filters;
import htsjdk.samtools.SAMRecord; import htsjdk.samtools.SAMRecord;
/** /**
* Filter out reads that are secondary alignments * Filter out reads that are non-primary alignments
* *
* <p>This filter recognizes the SAM flag that identifies secondary alignments (ie not the best alignment). * <p>This filter recognizes the SAM flag that identifies secondary and supplementary alignments, i.e. non-primary alignments.
* It is intended to ensure that only reads that are likely to be mapped in the right place, and therefore to be * It is intended to ensure that only reads that are likely to be mapped in the right place, and therefore to be
* informative, will be used in analysis.</p> * informative, will be used in analysis.</p>
* *
@ -53,4 +53,4 @@ public class NotPrimaryAlignmentFilter extends ReadFilter {
public boolean filterOut( final SAMRecord read ) { public boolean filterOut( final SAMRecord read ) {
return read.getNotPrimaryAlignmentFlag(); return read.getNotPrimaryAlignmentFlag();
} }
} }