From 7008a469dc0cdc2cdcb09c6c232df9a7705dfd9c Mon Sep 17 00:00:00 2001 From: hanna Date: Mon, 11 Oct 2010 03:01:04 +0000 Subject: [PATCH] Update MalformedReadFilter to pass reads that have cigar strings like 40S36I that have 0 aligned bases in the genome. We'll have to fix walkers as faults appear. Also added JIRA GSA-406: finer-grained control of MalformedReadFilter: want to exception out by default in these cases but pass them with a warning with a corresponding -U flag. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4476 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/filters/MalformedReadFilter.java | 6 +++--- .../broadinstitute/sting/gatk/traversals/TraverseReads.java | 1 - 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java index ca6387d8d..d56b8b780 100644 --- a/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java +++ b/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java @@ -72,8 +72,8 @@ public class MalformedReadFilter implements SamRecordHeaderFilter { * @return true if read end is valid, false otherwise. */ private static boolean checkInvalidAlignmentEnd( SAMRecord read ) { - // Alignment ends prior to its beginning - if( !read.getReadUnmappedFlag() && read.getAlignmentEnd() != -1 && read.getAlignmentEnd() < read.getAlignmentStart() ) + // Alignment aligns to negative number of bases in the reference. + if( !read.getReadUnmappedFlag() && read.getAlignmentEnd() != -1 && (read.getAlignmentEnd()-read.getAlignmentStart()+1)<0 ) return false; return true; } @@ -105,7 +105,7 @@ public class MalformedReadFilter implements SamRecordHeaderFilter { if( !read.getReadUnmappedFlag() && read.getAlignmentStart() != -1 && read.getAlignmentStart() != SAMRecord.NO_ALIGNMENT_START && - read.getAlignmentBlocks().size() == 0 ) + read.getAlignmentBlocks().size() < 0 ) return false; return true; } diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java index 31a85cc28..4cb5b4949 100755 --- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java +++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java @@ -92,7 +92,6 @@ public class TraverseReads extends TraversalEngine,Read // update the number of reads we've seen ReadMetrics readMetrics = dataProvider.getShard().getReadMetrics(); readMetrics.incrementNumIterations(); - readMetrics.incrementNumReadsSeen(); // if the read is mapped, create a metadata tracker ReadMetaDataTracker tracker = (read.getReferenceIndex() >= 0) ? rodView.getReferenceOrderedDataForRead(read) : null;