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Bug fix: single unmapped read now keeps mapping qual 0 after remapping, not 37! 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1557 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-09-09 15:29:34 +00:00
parent df11618092
commit 0721c450c2
1 changed files with 12 additions and 8 deletions
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20
java/src/org/broadinstitute/sting/playground/tools/RemapAlignments.java
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@ -128,12 +128,12 @@ public class RemapAlignments extends CommandLineProgram {
continue;
}
if ( AlignmentUtils.isReadUnmapped(read) ) totalUnmappedReads++;
else {
// destroy mate pair mapping information, if any (we will need to reconstitute pairs after remapping both ends):
read.setMateReferenceIndex(SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX);
read.setMateAlignmentStart(SAMRecord.NO_ALIGNMENT_START);
// destroy mate pair mapping information, if any (we will need to reconstitute pairs after remapping both ends):
read.setMateReferenceIndex(SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX);
read.setMateAlignmentStart(SAMRecord.NO_ALIGNMENT_START);
// if ( read.getReadPairedFlag() ) System.out.println("PAIRED READ!!");
}
totalRecords++;
if ( totalRecords % 1000000 == 0 ) System.out.println(totalRecords + " valid records processed");
@ -203,9 +203,13 @@ public class RemapAlignments extends CommandLineProgram {
// technically, if edit distance of the read is equal to max_diff used in alignments,
// we should have set 25...
r.setMappingQuality(37);
r.setAttribute("X0", new Integer(1));
r.setAttribute("X1", new Integer(0));
if ( AlignmentUtils.isReadUnmapped(r) ) {
r.setMappingQuality(0);
} else {
r.setMappingQuality(37);
r.setAttribute("X0", new Integer(1));
r.setAttribute("X1", new Integer(0));
}
r.setNotPrimaryAlignmentFlag(false);
} else {