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Simplified SAMRecord construction and emission. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@296 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-04-05 04:48:31 +00:00
parent 0d25e71953
commit f12d40dde8
1 changed files with 20 additions and 34 deletions
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54
java/src/org/broadinstitute/sting/playground/fourbasecaller/FourBaseRecaller.java
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@ -96,44 +96,30 @@ public class FourBaseRecaller extends CommandLineProgram {
nextbestqual[cycle] = QualityUtils.baseAndProbToCompressedQuality(fp.indexAtRank(1), fp.probAtRank(1));
}
SAMRecord sr = new SAMRecord(sfh);
sr.setReadName("KIR_" + bread.getReadName());
sr.setReadUmappedFlag(true);
sr.setReadBases(asciiseq);
sr.setBaseQualities(bestqual);
sr.setAttribute("SQ", nextbestqual);
sr.setReadFailsVendorQualityCheckFlag(!bread.isPf());
sr.setReadPairedFlag(isPaired);
if (isPaired) {
sr.setMateUnmappedFlag(true);
sr.setFirstOfPairFlag(END <= 1);
sr.setSecondOfPairFlag(END > 1);
}
sfw.addAlignment(sr);
sfw.addAlignment(constructSAMRecord("KIR_", new String(asciiseq), bestqual, nextbestqual, isPaired, END, bread, sfh));
sfw.addAlignment(constructSAMRecord("BUS_", bases, quals, null, isPaired, END, bread, sfh));
SAMRecord sr2 = new SAMRecord(sfh);
sr2.setReadName("BUS_" + bread.getReadName());
sr2.setReadUmappedFlag(true);
sr2.setReadString(bases);
sr2.setBaseQualities(quals);
sr2.setReadFailsVendorQualityCheckFlag(!bread.isPf());
sr2.setReadPairedFlag(isPaired);
if (isPaired) {
sr2.setMateUnmappedFlag(true);
sr2.setFirstOfPairFlag(END <= 1);
sr2.setSecondOfPairFlag(END > 1);
}
sfw.addAlignment(sr2);
/*
System.out.println(sr.format());
System.out.println(sr2.format());
System.out.println("\n");
*/
queryid++;
} while (queryid < CALLING_LIMIT && bfp.hasNext() && (bread = bfp.next()) != null);
return 0;
}
private SAMRecord constructSAMRecord(String readNamePrefix, String bases, byte[] bestqual, byte[] nextbestqual, boolean isPaired, int END, BustardReadData bread, SAMFileHeader sfh) {
SAMRecord sr = new SAMRecord(sfh);
sr.setReadName(readNamePrefix + bread.getReadName());
sr.setReadUmappedFlag(true);
sr.setReadString(bases);
sr.setBaseQualities(bestqual);
if (nextbestqual != null) { sr.setAttribute("SQ", nextbestqual); }
sr.setReadFailsVendorQualityCheckFlag(!bread.isPf());
if (isPaired) {
sr.setMateUnmappedFlag(true);
sr.setFirstOfPairFlag(END <= 1);
sr.setFirstOfPairFlag(END > 1);
}
return sr;
}
}