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Added the ability to specify the sorted, unaligned bam and/or the sorted, aligned bam such that broken computations can be restarted. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@805 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-05-22 19:33:34 +00:00
parent 454a6d1df7
commit 02c0afdb85
1 changed files with 60 additions and 36 deletions
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96
java/src/org/broadinstitute/sting/secondarybase/AnnotateSecondaryBase.java
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@ -49,6 +49,8 @@ public class AnnotateSecondaryBase extends CommandLineProgram {
@Argument(fullName="sam_in", shortName="SI", doc="The file to use for training and annotation", required=false) public File SAM_IN;
@Argument(fullName="training_limit", shortName="T", doc="Number of reads to use for parameter initialization", required=false) public int TRAINING_LIMIT = 100000;
@Argument(fullName="calling_limit", shortName="C", doc="Number of reads to basecall", required=false) public int CALLING_LIMIT = Integer.MAX_VALUE;
@Argument(fullName="unaligned_sam", shortName="US", doc="Unaligned sam file, so we can skip making it", required=false) public File USAM;
@Argument(fullName="aligned_sam", shortName="AS", doc="Aligned, queryname-sorted sam file, so we can skip resorting it", required=false) public File ASAM;
public static void main(String[] argv) {
Instance = new AnnotateSecondaryBase();
@ -57,61 +59,71 @@ public class AnnotateSecondaryBase extends CommandLineProgram {
protected int execute() {
ArrayList<Pair<Integer, Integer>> cycleRanges = getCycleRanges(CYCLE_RANGES);
File unalignedSam;
BasecallingTrainer trainer = new BasecallingTrainer(BUSTARD_DIR, LANE, TRAINING_LIMIT);
if (USAM == null || !USAM.exists()) {
BasecallingTrainer trainer = new BasecallingTrainer(BUSTARD_DIR, LANE, TRAINING_LIMIT);
// Iterate through raw Firecrest data and store the first unambiguous N reads up to TRAINING_LIMIT
System.out.println("Loading training set from the first " + TRAINING_LIMIT + " unambiguous reads in the raw data...");
trainer.loadFirstNUnambiguousReadsTrainingSet();
// Iterate through raw Firecrest data and store the first N reasonable reads up to TRAINING_LIMIT
System.out.println("Loading training set from the first " + TRAINING_LIMIT + " reasonable reads in the raw data...");
trainer.loadFirstNReasonableReadsTrainingSet();
// Iterate through the stored training data and add the info to the BasecallingReadModel
System.out.println("Applying training set...");
BasecallingReadModel model = new BasecallingReadModel(trainer.getTrainingData());
// Iterate through the stored training data and add the info to the BasecallingReadModel
System.out.println("Applying training set...");
BasecallingReadModel model = new BasecallingReadModel(trainer.getTrainingData());
// Call bases and write results
System.out.println("Calling bases...");
// Call bases and write results
System.out.println("Calling bases...");
SAMFileHeader sfh = new SAMFileHeader();
sfh.setSortOrder(SAMFileHeader.SortOrder.queryname);
File unalignedSam = (canAnnotate(SAM_IN)) ? getTempSAMFile("unaligned") : SAM_OUT;
SAMFileWriter sfw = new SAMFileWriterFactory().makeSAMOrBAMWriter(sfh, false, unalignedSam);
SAMFileHeader sfh = new SAMFileHeader();
sfh.setSortOrder(SAMFileHeader.SortOrder.queryname);
IlluminaParser iparser = new IlluminaParser(BUSTARD_DIR, LANE);
unalignedSam = (canAnnotate(SAM_IN)) ? getTempSAMFile("unaligned") : SAM_OUT;
SAMFileWriter sfw = new SAMFileWriterFactory().makeSAMOrBAMWriter(sfh, false, unalignedSam);
BasecallingStats bstats = new BasecallingStats();
IlluminaParser iparser = new IlluminaParser(BUSTARD_DIR, LANE);
BasecallingStats bstats = new BasecallingStats();
while (bstats.getReadsTotal() < CALLING_LIMIT && iparser.next()) {
RawRead rr = iparser.getRawRead();
FourProbRead fpr = model.call(rr);
while (bstats.getReadsTotal() < CALLING_LIMIT && iparser.next()) {
RawRead rr = iparser.getRawRead();
FourProbRead fpr = model.call(rr);
for (int cycleRangeIndex = 0; cycleRangeIndex < cycleRanges.size(); cycleRangeIndex++) {
Pair<Integer, Integer> cycleRange = cycleRanges.get(cycleRangeIndex);
for (int cycleRangeIndex = 0; cycleRangeIndex < cycleRanges.size(); cycleRangeIndex++) {
Pair<Integer, Integer> cycleRange = cycleRanges.get(cycleRangeIndex);
RawRead rrEnd = iparser.getSubset(cycleRange.getFirst(), cycleRange.getSecond());
FourProbRead fprEnd = fpr.getSubset(cycleRange.getFirst(), cycleRange.getSecond());
RawRead rrEnd = iparser.getSubset(cycleRange.getFirst(), cycleRange.getSecond());
FourProbRead fprEnd = fpr.getSubset(cycleRange.getFirst(), cycleRange.getSecond());
sfw.addAlignment(constructSAMRecord(rrEnd, fprEnd, sfh, RUN_BARCODE, cycleRanges.size() == 2, cycleRangeIndex == 1));
sfw.addAlignment(constructSAMRecord(rrEnd, fprEnd, sfh, RUN_BARCODE, cycleRanges.size() == 2, cycleRangeIndex == 1));
if (cycleRangeIndex == 0) {
bstats.update(rrEnd, fprEnd);
bstats.notifyOnInterval(5000);
if (cycleRangeIndex == 0) {
bstats.update(rrEnd, fprEnd);
bstats.notifyOnInterval(5000);
}
}
}
bstats.notifyNow();
iparser.close();
sfw.close();
} else {
unalignedSam = USAM;
}
bstats.notifyNow();
iparser.close();
sfw.close();
if (canAnnotate(SAM_IN)) {
// If we're in annotation mode, annotate the aligned BAM file with the SQ tag
System.out.println("Annotating aligned SAM file...");
System.out.println(" sorting aligned SAM file by read name...");
File alignedSam = getTempSAMFile("aligned");
sortBAMByReadName(SAM_IN, alignedSam);
File alignedSam;
if (ASAM == null || !ASAM.exists()) {
System.out.println(" sorting aligned SAM file by read name...");
alignedSam = getTempSAMFile("aligned");
sortBAMByReadName(SAM_IN, alignedSam);
} else {
alignedSam = ASAM;
}
System.out.println(" merging unaligned and aligned SAM files...");
File mergedSam = SAM_OUT;
@ -266,21 +278,30 @@ public class AnnotateSecondaryBase extends CommandLineProgram {
SAMRecord usr = usamIt.next();
SAMRecord asr = asamIt.next();
int annotatedRecords = 0;
do {
// Pull a record from the unaligned file and advance the aligned file until we find the matching record. We
// don't have to advance the unaligned file until we find our record because we assume every record we generate
// will be in the aligned file (which also contains unaligned reads).
//
// If Picard ever stops storing the unaligned reads, this logic will need to be rewritten.
System.out.println(asr.getReadString());
System.out.println(BaseUtils.simpleReverseComplement(asr.getReadString()));
System.out.println();
if (usr.getReadName().equals(asr.getReadName()) && usr.getFirstOfPairFlag() == asr.getFirstOfPairFlag()) {
byte[] sqtag = (byte[]) usr.getAttribute("SQ");
String usrread = usr.getReadString();
String asrread = asr.getReadString();
System.out.println(asrread);
if (asr.getReadNegativeStrandFlag()) {
sqtag = QualityUtils.reverseComplementCompressedQualityArray(sqtag);
asrread = BaseUtils.simpleReverseComplement(asrread);
System.out.println(asrread);
}
if (usrread != null && asrread != null && !usrread.equals(asrread)) {
@ -291,6 +312,9 @@ public class AnnotateSecondaryBase extends CommandLineProgram {
}
asr.setAttribute("SQ", sqtag);
annotatedRecords++;
System.out.println("Annotated " + annotatedRecords + " records.");
usr = usamIt.next();
} else {