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Comments for Ryan (which also apply to ReadQualityScoreWalker). 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1944 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-10-30 14:44:04 +00:00
parent ccd7440730
commit 51fffc7f69
1 changed files with 11 additions and 0 deletions
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11
java/src/org/broadinstitute/sting/playground/gatk/walkers/NeighborhoodQualityWalker.java
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@ -88,6 +88,8 @@ public class NeighborhoodQualityWalker extends LocusWalker<Integer, Long> {
List<SAMRecord> reads = context.getReads();
Iterator<SAMRecord> readsIter = reads.iterator();
// EB: the problem with "assert" in java is that it's disabled by default and you actively need
// to enable them on the command line (-ea), so we should really use a formal if statement.
assert reads.size() > 0 : "This locus has no reads.";
while( readsIter.hasNext() ) { // for each read in this context
@ -95,6 +97,9 @@ public class NeighborhoodQualityWalker extends LocusWalker<Integer, Long> {
// Only consider reads for this calculation whose mapping quality isn't 0 or 255
mappingQuality = read.getMappingQuality();
// EB: actually, mapping quality zero reads are crucial to this calculation as they
// affect the overall reliability of this neighborhood (i.e. the more of them that
// there are, the less we trust the alignments in the neighborhood).
if ( mappingQuality > 0 && mappingQuality < 255 ) {
// Generate sum of mapping quality for all reads at this locus
@ -103,10 +108,16 @@ public class NeighborhoodQualityWalker extends LocusWalker<Integer, Long> {
// Look to see if mate was mapped to different chromosome
//isGoodPair = ( read.getReadPairedFlag() ? read.getProperPairFlag() : true );
// EB: I'm pretty sure that getReadPairedFlag() just tells you whether the read has a mate
// I think you want to be checking getMateReferenceIndex() relative to this read's ref index
isGoodPair = ( !read.getReadPairedFlag() || read.getProperPairFlag() ); // optimized version of above line
if ( !isGoodPair ) { numReadsMismatchedMate++; }
// Generate sum number of mismatches for all reads at this locus
// EB: It turns out that the NM attribute is not always set correctly (Mark found several cases)
// so we can't trust it. Check out AlignmentUtils for several methods that already determine the number of mismatches.
if( read.getAttribute("NM") != null ) {
sumMismatchRate += ((float) Integer.parseInt(read.getAttribute("NM").toString())) / ((float) read.getReadLength());
} else {