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Some changes to the system for annotating a pre-aligned bam file. Doesn't fit within 2gigs. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@746 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-05-18 17:42:08 +00:00
parent a39c8839c8
commit 7c615c8fb0
1 changed files with 77 additions and 11 deletions
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88
java/src/org/broadinstitute/sting/secondarybase/AnnotateSecondaryBase.java
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@ -1,14 +1,13 @@
package org.broadinstitute.sting.secondarybase;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMFileWriter;
import net.sf.samtools.SAMFileWriterFactory;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.*;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.cmdLine.CommandLineProgram;
import java.io.File;
import java.util.HashMap;
/**
* AnnotateSecondaryBase computes the second best base for every base in an Illumina lane.
@ -56,32 +55,99 @@ public class AnnotateSecondaryBase extends CommandLineProgram {
model.train(trainingSet);
// Call bases and write results
System.out.println("Calling bases and writing SAM file...");
SAMFileHeader sfh = new SAMFileHeader();
SAMFileWriter sfw = new SAMFileWriterFactory().makeSAMOrBAMWriter(sfh, false, SAM_OUT);
BasecallingStats bstats = new BasecallingStats();
IlluminaParser iparser = new IlluminaParser(BUSTARD_DIR, LANE, CYCLE_BEGIN, CYCLE_END);
HashMap<String, byte[]> sqhash = null;
if (canAnnotate(SAM_IN)) {
System.out.println("Loading read names from aligned SAM file...");
sqhash = new HashMap<String, byte[]>(10000000);
SAMFileReader samIn = new SAMFileReader(SAM_IN);
for (SAMRecord sr : samIn) {
sqhash.put(sr.getReadName(), null);
}
samIn.close();
}
System.out.println("Calling bases...");
RawRead rr;
while (bstats.getReadsTotal() < CALLING_LIMIT && (rr = iparser.next()) != null) {
FourProbRead fpr = model.call(rr);
if (canAnnotate(SAM_IN)) {
String readname = String.format("%s:%s#0", RUN_BARCODE, rr.getReadKey());
sfw.addAlignment(constructSAMRecord(rr, fpr, sfh, RUN_BARCODE));
bstats.update(rr, fpr);
if (sqhash.containsKey(readname)) {
FourProbRead fpr = model.call(rr);
bstats.notifyOnInterval(10000);
byte[] sqtag = fpr.getSQTag(rr);
sqhash.put(readname, sqtag);
bstats.update(rr, fpr);
bstats.notifyOnInterval(10000);
}
} else {
FourProbRead fpr = model.call(rr);
sfw.addAlignment(constructSAMRecord(rr, fpr, sfh, RUN_BARCODE));
bstats.update(rr, fpr);
bstats.notifyOnInterval(10000);
}
}
iparser.close();
sfw.close();
bstats.notifyNow();
if (canAnnotate(SAM_IN)) {
// Correlate SQ tags with aligned SAM records:
System.out.println("Merge unaligned and aligned SAM files...");
SAMFileReader samIn = new SAMFileReader(SAM_IN);
for (SAMRecord sr : samIn) {
if (sqhash.containsKey(sr.getReadName())) {
byte[] sqtag = sqhash.get(sr.getReadName());
if (sqtag != null) {
if (sr.getReadNegativeStrandFlag()) {
QualityUtils.reverseComplementCompressedQualityArray(sqtag);
}
sr.setAttribute("SQ", sqtag);
}
}
sfw.addAlignment(sr);
}
samIn.close();
}
sfw.close();
System.out.println("Done.");
return 0;
}
/**
* Simple test to determine whether we're in aligned bam annotation mode or not.
*
* @param samfile the aligned sam file
* @return true if the file exists, false otherwise
*/
private boolean canAnnotate(File samfile) {
return (samfile != null && samfile.exists());
}
/**
* Construct a SAMRecord object with the specified information. The secondary bases
* will be annotated suchthat they will not conflict with the primary base.