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Now only distributes 80% of the residual probability to the secondary base, 10% each to the other two bases. Nicer labelling for stringified probability distribution output. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@521 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-04-24 03:34:43 +00:00
parent 3cda85f2e3
commit 135d3eabeb
1 changed files with 6 additions and 4 deletions
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10
java/src/org/broadinstitute/sting/utils/BasicPileup.java
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@ -159,11 +159,13 @@ abstract public class BasicPileup implements Pileup {
double epsilon = 1e-4;
int secondBestBaseIndex = QualityUtils.compressedQualityToBaseIndex(sqs[offset]);
dist[readIndex][secondBestBaseIndex] = (1.0 - dist[readIndex][bestBaseIndex] - 2.0*epsilon);
//dist[readIndex][secondBestBaseIndex] = (1.0 - dist[readIndex][bestBaseIndex] - 2.0*epsilon);
dist[readIndex][secondBestBaseIndex] = 0.8*(1.0 - dist[readIndex][bestBaseIndex]);
for (int baseIndex = 0; baseIndex < 4; baseIndex++) {
if (baseIndex != bestBaseIndex && baseIndex != secondBestBaseIndex) {
dist[readIndex][baseIndex] = epsilon;
//dist[readIndex][baseIndex] = epsilon;
dist[readIndex][baseIndex] = 0.1*(1.0 - dist[readIndex][bestBaseIndex]);
}
}
} else {
@ -186,11 +188,11 @@ abstract public class BasicPileup implements Pileup {
public static String probDistPileupAsString( List<SAMRecord> reads, List<Integer> offsets ) {
double[][] dist = probDistPileup(reads, offsets);
String distString = "";
String distString = String.format(" %c %c %c %c\n", 'A', 'C', 'G', 'T');
for (int readIndex = 0; readIndex < dist.length; readIndex++) {
distString += "[ ";
for (int baseIndex = 0; baseIndex < 4; baseIndex++) {
distString += String.format("%3.3f ", dist[readIndex][baseIndex]);
distString += String.format("%4.4f ", dist[readIndex][baseIndex]);
}
distString += "]\n";
}