From 135d3eabebbaef81c84ba6c70c5adb99de83c399 Mon Sep 17 00:00:00 2001 From: kiran Date: Fri, 24 Apr 2009 03:34:43 +0000 Subject: [PATCH] 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 --- .../org/broadinstitute/sting/utils/BasicPileup.java | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/java/src/org/broadinstitute/sting/utils/BasicPileup.java b/java/src/org/broadinstitute/sting/utils/BasicPileup.java index bf25bbab2..a9a769ae6 100755 --- a/java/src/org/broadinstitute/sting/utils/BasicPileup.java +++ b/java/src/org/broadinstitute/sting/utils/BasicPileup.java @@ -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 reads, List 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"; }