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Replaced dumb training function with a version that creates a training set slightly more sensibly. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@806 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-05-22 19:34:33 +00:00
parent 02c0afdb85
commit cd80e3f372
1 changed files with 20 additions and 3 deletions
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23
java/src/org/broadinstitute/sting/secondarybase/BasecallingTrainer.java
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@ -58,9 +58,10 @@ public class BasecallingTrainer {
} }
/** /**
* Take the first N reads that have no ambiguous bases and add them to the training set. * Take the first N reads that have no ambiguous bases, an average quality score greater
* than or equal to 15, and are not largely homopolymers and add them to the training set.
*/ */
public void loadFirstNUnambiguousReadsTrainingSet() { public void loadFirstNReasonableReadsTrainingSet() {
this.trainingData = new ArrayList<RawRead>(trainingLimit); this.trainingData = new ArrayList<RawRead>(trainingLimit);
IlluminaParser iparser = new IlluminaParser(bustardDir, lane); IlluminaParser iparser = new IlluminaParser(bustardDir, lane);
@ -80,13 +81,29 @@ public class BasecallingTrainer {
} }
} }
if (numAmbiguous == 0) { if (numAmbiguous == 0 && getAverageQualityScore(rawread) >= 15 && BaseUtils.mostFrequentBaseFraction(rawread.getSequence()) < 0.4) {
trainingData.add(rawread); trainingData.add(rawread);
numreads++; numreads++;
} }
} }
} }
/**
* Return the average quality score of a raw read.
*
* @param read the raw read
* @return the average quality score
*/
private double getAverageQualityScore(RawRead read) {
double averageQual = 0;
for ( byte qual : read.getQuals() ) {
averageQual += qual;
}
return averageQual / ((double) read.getReadLength());
}
/** /**
* Load a training set from perfect reads in an already-aligned bam file. * Load a training set from perfect reads in an already-aligned bam file.
* *