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Fixes for including duplicate reads in the locus traversal; now checks that the ref arg is provided when needed 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@459 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-04-17 01:27:36 +00:00
parent e842b543c9
commit dbf2344cef
3 changed files with 11 additions and 0 deletions
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4
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
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@ -251,6 +251,10 @@ public class GenomeAnalysisTK extends CommandLineProgram {
try { try {
LocusWalker<?, ?> walker = (LocusWalker<?, ?>) my_walker; LocusWalker<?, ?> walker = (LocusWalker<?, ?>) my_walker;
if ( REF_FILE_ARG == null )
Utils.scareUser(String.format("Locus-based traversals require a reference file but none was given"));
if ( INPUT_FILE == null ) { if ( INPUT_FILE == null ) {
if ( walker.requiresReads() ) if ( walker.requiresReads() )
Utils.scareUser(String.format("Analysis %s requires reads, but none were given", Analysis_Name)); Utils.scareUser(String.format("Analysis %s requires reads, but none were given", Analysis_Name));

5
java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
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@ -275,6 +275,7 @@ public abstract class TraversalEngine {
TraversalStatistics.nReads, TraversalStatistics.nReads,
(TraversalStatistics.nSkippedReads * 100.0) / TraversalStatistics.nReads)); (TraversalStatistics.nSkippedReads * 100.0) / TraversalStatistics.nReads));
logger.info(String.format(" -> %d unmapped reads", TraversalStatistics.nUnmappedReads)); logger.info(String.format(" -> %d unmapped reads", TraversalStatistics.nUnmappedReads));
logger.info(String.format(" -> %d duplicate reads", TraversalStatistics.nDuplicates));
logger.info(String.format(" -> %d non-primary reads", TraversalStatistics.nNotPrimary)); logger.info(String.format(" -> %d non-primary reads", TraversalStatistics.nNotPrimary));
logger.info(String.format(" -> %d reads with bad alignments", TraversalStatistics.nBadAlignments)); logger.info(String.format(" -> %d reads with bad alignments", TraversalStatistics.nBadAlignments));
logger.info(String.format(" -> %d reads with indels", TraversalStatistics.nSkippedIndels)); logger.info(String.format(" -> %d reads with indels", TraversalStatistics.nSkippedIndels));
@ -490,6 +491,10 @@ public abstract class TraversalEngine {
TraversalStatistics.nBadAlignments++; TraversalStatistics.nBadAlignments++;
result = true; result = true;
why = "No alignment start"; why = "No alignment start";
} else if (rec.getDuplicateReadFlag()) {
TraversalStatistics.nDuplicates++;
result = true;
why = "Duplicate reads";
} }
else { else {
result = false; result = false;

2
java/src/org/broadinstitute/sting/gatk/traversals/TraversalStatistics.java
View File

@ -19,6 +19,7 @@ public class TraversalStatistics {
public static int nNotPrimary; public static int nNotPrimary;
public static int nBadAlignments; public static int nBadAlignments;
public static int nSkippedIndels; public static int nSkippedIndels;
public static int nDuplicates;
static { static {
reset(); reset();
@ -32,5 +33,6 @@ public class TraversalStatistics {
nNotPrimary = 0; nNotPrimary = 0;
nBadAlignments = 0; nBadAlignments = 0;
nSkippedIndels = 0; nSkippedIndels = 0;
nDuplicates = 0;
} }
} }