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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
This commit is contained in:
hanna 2010-03-08 22:44:54 +00:00
parent 81ffb8243d
commit 02f48b6457
2 changed files with 8 additions and 7 deletions
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14
java/src/org/broadinstitute/sting/gatk/traversals/TraversalStatistics.java
View File

@ -13,13 +13,13 @@ public class TraversalStatistics {
// Number of records (loci, reads) we've processed // Number of records (loci, reads) we've processed
public static long nRecords; public static long nRecords;
// How many reads have we processed, along with those skipped for various reasons // How many reads have we processed, along with those skipped for various reasons
public static int nReads; public static long nReads;
public static int nSkippedReads; public static long nSkippedReads;
public static int nUnmappedReads; public static long nUnmappedReads;
public static int nNotPrimary; public static long nNotPrimary;
public static int nBadAlignments; public static long nBadAlignments;
public static int nSkippedIndels; public static long nSkippedIndels;
public static int nDuplicates; public static long nDuplicates;
static { static {
reset(); reset();

1
java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java
View File

@ -96,6 +96,7 @@ public class TraverseReads extends TraversalEngine {
// update the number of reads we've seen // update the number of reads we've seen
TraversalStatistics.nRecords++; TraversalStatistics.nRecords++;
TraversalStatistics.nReads++;
// if the read is mapped, create a metadata tracker // if the read is mapped, create a metadata tracker
ReadMetaDataTracker tracker = (read.getReferenceIndex() >= 0) ? rodView.getReferenceOrderedDataForRead(read) : null; ReadMetaDataTracker tracker = (read.getReferenceIndex() >= 0) ? rodView.getReferenceOrderedDataForRead(read) : null;