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Wrote a public static version of loadFirstNReasonableReadsTrainingSet() so Alec can call it. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1046 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-06-18 20:18:17 +00:00
parent a4fa02f11c
commit 03fe166994
1 changed files with 36 additions and 1 deletions
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37
java/src/org/broadinstitute/sting/secondarybase/BasecallingTrainer.java
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@ -88,13 +88,48 @@ public class BasecallingTrainer {
}
}
/**
* 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.
*
* @param bustardDir the bustard directory
* @param lane the lane number
* @param trainingLimit how many reads should we use to train?
*/
public static void loadNReasonableReadsTrainingSet(File bustardDir, int lane, int trainingLimit) {
ArrayList<RawRead> trainingData = new ArrayList<RawRead>(trainingLimit);
IlluminaParser iparser = new IlluminaParser(bustardDir, lane);
RawRead rawread;
int numreads = 0;
while (numreads < trainingLimit && iparser.next()) {
rawread = iparser.getRawRead();
int numAmbiguous = 0;
byte[] sequence = rawread.getSequence();
for ( byte byteBase : sequence ) {
if (BaseUtils.simpleBaseToBaseIndex((char) byteBase) == -1) {
numAmbiguous++;
}
}
if (numAmbiguous == 0 && getAverageQualityScore(rawread) >= 15 && BaseUtils.mostFrequentBaseFraction(rawread.getSequence()) < 0.4) {
trainingData.add(rawread);
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) {
private static double getAverageQualityScore(RawRead read) {
double averageQual = 0;
for ( byte qual : read.getQuals() ) {