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Updated to use SecondaryBaseAnnotator class. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1126 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-06-30 16:08:43 +00:00
parent e3cdf7ef4b
commit d412c5dc2f
1 changed files with 91 additions and 41 deletions
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132
java/src/org/broadinstitute/sting/playground/piecemealannotator/TileAnnotator.java
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@ -1,10 +1,7 @@
package org.broadinstitute.sting.playground.piecemealannotator; package org.broadinstitute.sting.playground.piecemealannotator;
import net.sf.samtools.*; import net.sf.samtools.*;
import org.broadinstitute.sting.secondarybase.BasecallingReadModel; import org.broadinstitute.sting.secondarybase.*;
import org.broadinstitute.sting.secondarybase.BasecallingStats;
import org.broadinstitute.sting.secondarybase.FourProbRead;
import org.broadinstitute.sting.secondarybase.RawRead;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.Pair; import org.broadinstitute.sting.utils.Pair;
import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.utils.StingException;
@ -44,53 +41,19 @@ public class TileAnnotator extends CommandLineProgram {
protected int execute() { protected int execute() {
ArrayList<Pair<Integer, Integer>> cycleRanges = getCycleRanges(CYCLE_RANGES); ArrayList<Pair<Integer, Integer>> cycleRanges = getCycleRanges(CYCLE_RANGES);
SecondaryBaseAnnotator sba = new SecondaryBaseAnnotator();
System.out.printf("%s: Loading training set...\n", (new Date()).toString()); System.out.printf("%s: Loading training set...\n", (new Date()).toString());
ArrayList<RawRead> trainingData = loadTrainingData(); loadTrainingData(sba);
System.out.printf("%s: Training model...\n", (new Date()).toString());
BasecallingReadModel model = new BasecallingReadModel(trainingData);
System.out.printf("%s: Calling bases...\n", (new Date()).toString()); System.out.printf("%s: Calling bases...\n", (new Date()).toString());
callBases(model, cycleRanges); callBases(sba, cycleRanges);
System.out.println("Done."); System.out.println("Done.");
return 0; return 0;
} }
//private void callBases(BasecallingReadModel model, ArrayList<Pair<Integer, Integer>> cycleRanges, ArrayList<RawRead> trainingData) {
private void callBases(BasecallingReadModel model, ArrayList<Pair<Integer, Integer>> cycleRanges) {
SAMFileHeader sheader = new SAMFileHeader();
sheader.setSortOrder(SAMFileHeader.SortOrder.unsorted);
SAMFileWriter swriter = new SAMFileWriterFactory().makeSAMOrBAMWriter(sheader, true, SAM_TILE_OUT);
IlluminaTile tileParser = new IlluminaTile(BUSTARD_DIR, lane, tile);
BasecallingStats bstats = new BasecallingStats();
for (RawRead rr : tileParser) {
FourProbRead fpr = model.call(rr);
for (int rangeIndex = 0; rangeIndex < cycleRanges.size(); rangeIndex++) {
FourProbRead fprEnd = fpr.getSubset(cycleRanges.get(rangeIndex).getFirst(), cycleRanges.get(rangeIndex).getSecond());
RawRead rrEnd = rr.getSubset(cycleRanges.get(rangeIndex).getFirst(), cycleRanges.get(rangeIndex).getSecond());
SAMRecord sr = constructSAMRecord(rrEnd, fprEnd, sheader, cycleRanges.size() > 1, rangeIndex == 1);
swriter.addAlignment(sr);
}
bstats.update(rr, fpr);
bstats.notifyOnInterval(10000);
}
bstats.notifyNow();
tileParser.close();
swriter.close();
}
private ArrayList<Pair<Integer, Integer>> getCycleRanges(String cycleRangesString) { private ArrayList<Pair<Integer, Integer>> getCycleRanges(String cycleRangesString) {
ArrayList< Pair<Integer, Integer> > cycleRanges = new ArrayList< Pair<Integer, Integer> >(); ArrayList< Pair<Integer, Integer> > cycleRanges = new ArrayList< Pair<Integer, Integer> >();
@ -120,6 +83,61 @@ public class TileAnnotator extends CommandLineProgram {
return cycleRanges; return cycleRanges;
} }
private void loadTrainingData(SecondaryBaseAnnotator sba) {
IlluminaTile tileParser = new IlluminaTile(BUSTARD_DIR, lane, tile);
for (RawRead rr : tileParser) { sba.addTrainingRead(rr); }
tileParser.close();
sba.doneTraining();
}
private void callBases(SecondaryBaseAnnotator sba, ArrayList<Pair<Integer, Integer>> cycleRanges) {
SAMFileHeader sheader = new SAMFileHeader();
sheader.setSortOrder(SAMFileHeader.SortOrder.unsorted);
SAMFileWriter swriter = new SAMFileWriterFactory().makeSAMOrBAMWriter(sheader, true, SAM_TILE_OUT);
IlluminaTile tileParser = new IlluminaTile(BUSTARD_DIR, lane, tile);
BasecallingStats bstats = new BasecallingStats();
for (RawRead rr : tileParser) {
bstats.update(rr, sba.getFourProbRead(rr));
byte[] sqtag = sba.getSqTagValue(rr);
SAMRecord sr = constructSAMRecord(rr, sqtag, sheader, false, false);
swriter.addAlignment(sr);
}
bstats.notifyNow();
tileParser.close();
swriter.close();
}
private SAMRecord constructSAMRecord(RawRead rr, byte[] sqtag, SAMFileHeader sfh, boolean isPaired, boolean isSecondEndOfPair) {
SAMRecord sr = new SAMRecord(sfh);
sr.setReadName(String.format("%s:%d:%d:%d:%d#0", RUN_BARCODE, lane, tile, rr.getXCoordinate(), rr.getYCoordinate()));
sr.setReadUmappedFlag(true);
sr.setReadString(rr.getSequenceAsString());
sr.setBaseQualities(rr.getQuals());
sr.setAttribute("SQ", sqtag);
sr.setReadPairedFlag(isPaired);
if (isPaired) {
sr.setMateUnmappedFlag(true);
sr.setFirstOfPairFlag(!isSecondEndOfPair);
sr.setSecondOfPairFlag(isSecondEndOfPair);
}
return sr;
}
/*
private SAMRecord constructSAMRecord(RawRead rr, FourProbRead fpr, SAMFileHeader sfh, boolean isPaired, boolean isSecondEndOfPair) { private SAMRecord constructSAMRecord(RawRead rr, FourProbRead fpr, SAMFileHeader sfh, boolean isPaired, boolean isSecondEndOfPair) {
SAMRecord sr = new SAMRecord(sfh); SAMRecord sr = new SAMRecord(sfh);
@ -139,6 +157,37 @@ public class TileAnnotator extends CommandLineProgram {
return sr; return sr;
} }
private void callBases(BasecallingReadModel model, ArrayList<Pair<Integer, Integer>> cycleRanges) {
SAMFileHeader sheader = new SAMFileHeader();
sheader.setSortOrder(SAMFileHeader.SortOrder.unsorted);
SAMFileWriter swriter = new SAMFileWriterFactory().makeSAMOrBAMWriter(sheader, true, SAM_TILE_OUT);
IlluminaTile tileParser = new IlluminaTile(BUSTARD_DIR, lane, tile);
BasecallingStats bstats = new BasecallingStats();
for (RawRead rr : tileParser) {
FourProbRead fpr = model.call(rr);
for (int rangeIndex = 0; rangeIndex < cycleRanges.size(); rangeIndex++) {
FourProbRead fprEnd = fpr.getSubset(cycleRanges.get(rangeIndex).getFirst(), cycleRanges.get(rangeIndex).getSecond());
RawRead rrEnd = rr.getSubset(cycleRanges.get(rangeIndex).getFirst(), cycleRanges.get(rangeIndex).getSecond());
SAMRecord sr = constructSAMRecord(rrEnd, fprEnd, sheader, cycleRanges.size() > 1, rangeIndex == 1);
swriter.addAlignment(sr);
}
bstats.update(rr, fpr);
bstats.notifyOnInterval(10000);
}
bstats.notifyNow();
tileParser.close();
swriter.close();
}
private ArrayList<RawRead> loadTrainingData() { private ArrayList<RawRead> loadTrainingData() {
FastaSequenceFile2 ref = new FastaSequenceFile2(REFERENCE); FastaSequenceFile2 ref = new FastaSequenceFile2(REFERENCE);
HashMap<String, SAMRecord> srs = loadTileAlignments(ref); HashMap<String, SAMRecord> srs = loadTileAlignments(ref);
@ -268,4 +317,5 @@ public class TileAnnotator extends CommandLineProgram {
return trainingData; return trainingData;
} }
*/
} }