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- get leftmost position of indel correct 

- don't try to clean reads with mapping quality of 0
- un-deprecate


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@813 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-05-26 17:24:58 +00:00
parent 54bb643d19
commit c2df35b7fe
1 changed files with 5 additions and 4 deletions
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9
java/src/org/broadinstitute/sting/playground/gatk/walkers/IntervalCleanerWalker.java
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@ -32,7 +32,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
public static final int MAX_QUAL = 99;
private SAMFileWriter writer;
private FileWriter indelOutput = null;
private FileWriter indelOutput = null;
// we need to sort the reads ourselves because SAM headers get messed up and claim to be "unsorted" sometimes
private TreeSet<ComparableSAMRecord> readsToWrite;
@ -69,6 +69,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
!read.getReadUnmappedFlag() &&
!read.getNotPrimaryAlignmentFlag() &&
!read.getDuplicateReadFlag() &&
read.getMappingQuality() != 0 &&
read.getAlignmentStart() != SAMRecord.NO_ALIGNMENT_START )
goodReads.add(read);
else
@ -271,7 +272,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
if ( indelOutput != null && bestConsensus.cigar.numCigarElements() > 1 ) {
StringBuffer str = new StringBuffer();
str.append(reads.get(0).getReferenceName());
int position = bestConsensus.positionOnReference + bestConsensus.cigar.getCigarElement(0).getLength();
int position = bestConsensus.positionOnReference + bestConsensus.cigar.getCigarElement(0).getLength() - 1;
str.append(":" + (leftmostIndex + position));
CigarElement ce = bestConsensus.cigar.getCigarElement(1);
str.append("\t" + ce.getLength() + ce.getOperator());
@ -462,7 +463,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
String reference = "AAAAAACCCCCCAAAAAA";
// the alternate reference is: "AAAAAACCCTTCCCAAAAAA";
ArrayList<SAMRecord> reads = new ArrayList<SAMRecord>();
SAMFileHeader header = getToolkit().getSamReader().getFileHeader();
SAMFileHeader header = getToolkit().getEngine().getSAMHeader();
SAMRecord r1 = new SAMRecord(header);
r1.setReadName("1");
r1.setReadString("AACCCCCC");
@ -512,7 +513,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
String reference = "AAAAAACCCTTCCCAAAAAA";
// the alternate reference is: "AAAAAACCCCCCAAAAAA";
ArrayList<SAMRecord> reads = new ArrayList<SAMRecord>();
SAMFileHeader header = getToolkit().getSamReader().getFileHeader();
SAMFileHeader header = getToolkit().getEngine().getSAMHeader();
SAMRecord r1 = new SAMRecord(header);
r1.setReadName("1");
r1.setReadString("ACCCTTCC");