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Aesthetic cleanup. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@735 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-05-17 04:09:23 +00:00
parent a0464633fd
commit 28bf7ec8ad
2 changed files with 35 additions and 11 deletions
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11
java/src/org/broadinstitute/sting/secondarybase/AnnotateSecondaryBase.java
View File

@ -36,7 +36,6 @@ public class AnnotateSecondaryBase extends CommandLineProgram {
@Argument(fullName="cycle_end", shortName="CE", doc="On what cycle does the read end? (0-based inclusive)") public int CYCLE_END;
@Argument(fullName="tlim", shortName="T", doc="Number of reads to use for parameter initialization", required=false) public int TRAINING_LIMIT = 250000;
@Argument(fullName="clim", shortName="C", doc="Number of reads to basecall", required=false) public int CALLING_LIMIT = Integer.MAX_VALUE;
@Argument(fullName="context", shortName="X", doc="Attempt to correct for context?", required=false) public Boolean CONTEXT = false;
@Argument(fullName="runbarcode", shortName="B", doc="Run barcode (embedded as part of the read name") public String RUN_BARCODE;
public static void main(String[] argv) {
@ -48,12 +47,12 @@ public class AnnotateSecondaryBase extends CommandLineProgram {
BasecallingTrainingSet trainingSet = new BasecallingTrainingSet(BUSTARD_DIR, LANE, CYCLE_BEGIN, CYCLE_END, TRAINING_LIMIT);
// Iterate through raw Firecrest data and store the first N reads up to TRAINING_LIMIT
System.out.println("Loading training set from the first " + TRAINING_LIMIT + " reads in the raw data...");
System.out.println("Loading training set from the first " + TRAINING_LIMIT + " unambiguous reads in the raw data...");
trainingSet.loadFirstNUnambiguousReadsTrainingSet();
// Iterate through the stored training data and add the info to the BasecallingReadModel
System.out.println("Applying training set...");
BasecallingReadModel model = new BasecallingReadModel(CYCLE_END - CYCLE_BEGIN + 1, CONTEXT);
BasecallingReadModel model = new BasecallingReadModel(CYCLE_END - CYCLE_BEGIN + 1, true);
model.train(trainingSet);
// Call bases and write results
@ -69,13 +68,15 @@ public class AnnotateSecondaryBase extends CommandLineProgram {
FourProbRead fpr = model.call(rr);
sfw.addAlignment(constructSAMRecord(rr, fpr, sfh, RUN_BARCODE));
bstats.update(rr, fpr, 10000);
bstats.update(rr, fpr);
bstats.notifyOnInterval(10000);
}
iparser.close();
sfw.close();
System.out.printf("%% bases consistent: %d/%d (%4.4f)\n", bstats.getBasesConsistent(), bstats.getBasesTotal(), bstats.getPercentConsistent());
bstats.notifyNow();
System.out.println("Done.");
return 0;

35
java/src/org/broadinstitute/sting/secondarybase/BasecallingStats.java
View File

@ -51,7 +51,7 @@ public class BasecallingStats {
* @return the percent of bases called consistently
*/
public double getPercentConsistent() {
return ((double) getBasesConsistent())/((double) getBasesTotal());
return 100.0*((double) getBasesConsistent())/((double) getBasesTotal());
}
/**
@ -60,7 +60,7 @@ public class BasecallingStats {
* @param rr the raw Illumina read
* @param fpr the FourProb read
*/
public void update(RawRead rr, FourProbRead fpr, int updateInterval) {
public void update(RawRead rr, FourProbRead fpr) {
for (int cycle = 0; cycle < fpr.size(); cycle++) {
int rawBaseIndex = BaseUtils.simpleBaseToBaseIndex((char) rr.getSequence()[cycle]);
int fpBaseIndex = fpr.get(cycle).indexAtRank(0);
@ -74,10 +74,33 @@ public class BasecallingStats {
}
}
if (basesTotal % updateInterval == 0 && basesTotal > 0) {
System.out.printf("%% bases consistent: %d/%d (%4.4f)\r", basesConsistent, basesTotal, ((double) basesConsistent)/((double) basesTotal));
}
readsTotal++;
}
/**
* Returns basecalling stats info in a nicely formatted string
*
* @return nicely formatted string containing basecalling stats
*/
public String toString() {
return String.format("%% bases consistent: %d/%d (%2.2f%%)", getBasesConsistent(), getBasesTotal(), getPercentConsistent());
}
/**
* Periodically print a line containing basecalling stats
*
* @param interval the periodicity of the messages given in number of bases observed
*/
public void notifyOnInterval(int interval) {
if (getBasesTotal() > 0 && getBasesTotal() % interval == 0) {
System.out.printf("%s\r", toString());
}
}
/**
* Immediately print a line containing basecalling stats
*/
public void notifyNow() {
System.out.printf("%s\n", toString());
}
}