From bfc40f54f0ae54e6bf679b349afb15779e606b7f Mon Sep 17 00:00:00 2001 From: kiran Date: Fri, 15 May 2009 20:07:08 +0000 Subject: [PATCH] Nicer output when training off of perfect reads. Not that that works yet... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@722 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/secondarybase/BasecallingTrainingSet.java | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/java/src/org/broadinstitute/sting/secondarybase/BasecallingTrainingSet.java b/java/src/org/broadinstitute/sting/secondarybase/BasecallingTrainingSet.java index c0ae20ca8..c2a5f39b7 100755 --- a/java/src/org/broadinstitute/sting/secondarybase/BasecallingTrainingSet.java +++ b/java/src/org/broadinstitute/sting/secondarybase/BasecallingTrainingSet.java @@ -182,6 +182,8 @@ public class BasecallingTrainingSet { IlluminaParser iparser = new IlluminaParser(bustardDir, lane, cycleBegin, cycleEnd); + int totalReadCount = 0; + for (int tile = 1; tile < trainingReads.size(); tile++) { iparser.seekToTile(tile); @@ -192,6 +194,13 @@ public class BasecallingTrainingSet { String readKey = iread.getReadKey(); if (trainingReads.get(tile).containsKey(readKey)) { + System.out.printf("\tTile %d: found %d of %d (%4.4f in tile, %4.4f total) \r", + tile, + tileReadCount, + trainingReads.get(tile).size(), + ((double) tileReadCount)/((double) trainingReads.get(tile).size()), + ((double) totalReadCount)/((double) trainingLimit)); + byte[] quals = new byte[iread.getReadLength()]; for (int qualIndex = 0; qualIndex < quals.length; qualIndex++) { quals[qualIndex] = 40; @@ -201,6 +210,7 @@ public class BasecallingTrainingSet { newTrainingData.add(iread); tileReadCount++; + totalReadCount++; } } }