From 2c57721ed2601c29ecacfe79fb56a844f1fc1b45 Mon Sep 17 00:00:00 2001 From: ebanks Date: Mon, 6 Jun 2011 01:04:07 +0000 Subject: [PATCH] Updated printouts to help with debugging. Issue does appear to be deterministic though. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5950 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/indels/IndelRealigner.java | 23 +++++++------------ 1 file changed, 8 insertions(+), 15 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java index e88a3cdcf..797af9ff3 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java @@ -641,11 +641,6 @@ public class IndelRealigner extends ReadWalker { // if there are any known indels for this region, get them and create alternate consenses generateAlternateConsensesFromKnownIndels(altConsenses, leftmostIndex, reference); - // TODO -- REMOVE ME WHEN WE FIND THE NON-DETERMINISM - if ( OUT_STATS != null ) { - logger.warn("ERIC: reads.size() = " + reads.size()); - } - // decide which reads potentially need to be cleaned; // if there are reads with a single indel in them, add that indel to the list of alternate consenses long totalRawMismatchSum = determineReadsThatNeedCleaning(reads, refReads, altReads, altAlignmentsToTest, altConsenses, leftmostIndex, reference); @@ -656,11 +651,6 @@ public class IndelRealigner extends ReadWalker { // if ( debugOn ) System.out.println("------\nChecking consenses...\n--------\n"); - // TODO -- REMOVE ME WHEN WE FIND THE NON-DETERMINISM - if ( OUT_STATS != null ) { - logger.warn("ERIC: altConsenses.size() after seeing reads = " + altConsenses.size()); - } - Consensus bestConsensus = null; Iterator iter = altConsenses.iterator(); @@ -872,11 +862,6 @@ public class IndelRealigner extends ReadWalker { continue; } - // TODO -- REMOVE ME WHEN WE FIND THE NON-DETERMINISM - if ( OUT_STATS != null ) { - logger.warn("ERIC: read = " + read.getReadName() + " " + read.getCigarString()); - } - final AlignedRead aRead = new AlignedRead(read); // first, move existing indels (for 1 indel reads only) to leftmost position within identical sequence @@ -1582,6 +1567,14 @@ public class IndelRealigner extends ReadWalker { loc = getToolkit().getGenomeLocParser().createGenomeLoc(loc.getContig(), padLeft, padRight); reference = referenceReader.getSubsequenceAt(loc.getContig(), loc.getStart(), loc.getStop()).getBases(); StringUtil.toUpperCase(reference); + + // TODO -- REMOVE ME WHEN WE FIND THE NON-DETERMINISM + if ( OUT_STATS != null ) { + logger.warn("ERIC: padLeft = " + padLeft); + logger.warn("ERIC: padRight = " + padRight); + logger.warn("ERIC: loc = " + loc); + logger.warn("ERIC: reference = " + new String(reference)); + } } return reference;