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I forgot that this depends on BoundedScoringSet. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1087 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-06-24 17:18:53 +00:00
parent 61ce4e5983
commit 69dc502174
1 changed files with 1 additions and 28 deletions
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29
java/src/org/broadinstitute/sting/playground/piecemealannotator/TileAnnotator.java
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@ -8,6 +8,7 @@ import org.broadinstitute.sting.secondarybase.RawRead;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.Pair;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.containers.BoundedScoringSet;
import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.cmdLine.CommandLineProgram;
import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2;
@ -25,8 +26,6 @@ public class TileAnnotator extends CommandLineProgram {
private String currentContig = "";
private byte[] refbases;
//private int lane;
//private int tile;
@Argument(fullName="sam_tile_in", shortName="STI", doc="SAM tile file", required=false) public File SAM_TILE_IN;
@Argument(fullName="sam_tile_out", shortName="STO", doc="Annotated SAM tile output file") public File SAM_TILE_OUT;
@ -53,7 +52,6 @@ public class TileAnnotator extends CommandLineProgram {
BasecallingReadModel model = new BasecallingReadModel(trainingData);
System.out.printf("%s: Calling bases...\n", (new Date()).toString());
//callBases(model, cycleRanges, trainingData);
callBases(model, cycleRanges);
System.out.println("Done.");
@ -71,28 +69,18 @@ public class TileAnnotator extends CommandLineProgram {
BasecallingStats bstats = new BasecallingStats();
//for (RawRead rr : trainingData) {
for (RawRead rr : tileParser) {
FourProbRead fpr = model.call(rr);
//System.out.println(rr.getSequenceAsString());
//System.out.println(fpr.getPrimaryBaseSequence());
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());
//System.out.println(rangeIndex + " : " + cycleRanges.get(rangeIndex).getFirst() + " " + cycleRanges.get(rangeIndex).getSecond());
//System.out.println(rrEnd.getSequenceAsString());
//System.out.println(fprEnd.getPrimaryBaseSequence());
SAMRecord sr = constructSAMRecord(rrEnd, fprEnd, sheader, cycleRanges.size() > 1, rangeIndex == 1);
swriter.addAlignment(sr);
}
//System.out.println();
bstats.update(rr, fpr);
bstats.notifyOnInterval(10000);
}
@ -227,10 +215,7 @@ public class TileAnnotator extends CommandLineProgram {
if (offset + readbases.length < refbases.length) {
valid = true;
//String refString = "";
for (int i = offset, j = 0; i < offset + readbases.length; i++, j++) {
//refString += (char) refbases[i - 1];
int refbase = BaseUtils.simpleBaseToBaseIndex((char) refbases[i - 1]);
int readbase = BaseUtils.simpleBaseToBaseIndex((char) readbases[j]);
@ -269,20 +254,8 @@ public class TileAnnotator extends CommandLineProgram {
} else {
additionalData.add(rr);
}
//trainingData.add(rr);
//if (trainingData.size() % 10000 == 0) {
// System.out.printf(" loaded %d reads\n", trainingData.size());
//}
}
//System.out.printf(" loaded %d reads\n", trainingData.size());
//for (RawRead rr : additionalData.toArray(new RawRead[0])) {
// System.out.println(rr.getSequenceAsString());
//}
tileParser.close();
System.out.printf(" found %d perfect reads with an optional reservoir of %d good reads\n", trainingData.size(), additionalData.size());