From 02f48b64570f6a37cbc099845c860783eb78c889 Mon Sep 17 00:00:00 2001 From: hanna Date: Mon, 8 Mar 2010 22:44:54 +0000 Subject: [PATCH] Fix bug that's been in the GATK for a very long time: update nReads (as well as nRecords), so that INFO logging doesn't say 'skipped 0 of 0 reads'. While I'm in there, update TraversalStatistics to store longs. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2959 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/traversals/TraversalStatistics.java | 14 +++++++------- .../sting/gatk/traversals/TraverseReads.java | 1 + 2 files changed, 8 insertions(+), 7 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalStatistics.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalStatistics.java index 2dfb9ad75..ee8a3e684 100755 --- a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalStatistics.java +++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalStatistics.java @@ -13,13 +13,13 @@ public class TraversalStatistics { // Number of records (loci, reads) we've processed public static long nRecords; // How many reads have we processed, along with those skipped for various reasons - public static int nReads; - public static int nSkippedReads; - public static int nUnmappedReads; - public static int nNotPrimary; - public static int nBadAlignments; - public static int nSkippedIndels; - public static int nDuplicates; + public static long nReads; + public static long nSkippedReads; + public static long nUnmappedReads; + public static long nNotPrimary; + public static long nBadAlignments; + public static long nSkippedIndels; + public static long nDuplicates; static { reset(); diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java index 9be830b34..58e1d319d 100755 --- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java +++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java @@ -96,6 +96,7 @@ public class TraverseReads extends TraversalEngine { // update the number of reads we've seen TraversalStatistics.nRecords++; + TraversalStatistics.nReads++; // if the read is mapped, create a metadata tracker ReadMetaDataTracker tracker = (read.getReferenceIndex() >= 0) ? rodView.getReferenceOrderedDataForRead(read) : null;