zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
View File

@ -251,6 +251,10 @@ public class GenomeAnalysisTK extends CommandLineProgram {
try {
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 ( walker.requiresReads() )
Utils.scareUser(String.format("Analysis %s requires reads, but none were given", Analysis_Name));

5
java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
View File

@ -275,6 +275,7 @@ public abstract class TraversalEngine {
TraversalStatistics.nReads,
(TraversalStatistics.nSkippedReads * 100.0) / TraversalStatistics.nReads));
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 reads with bad alignments", TraversalStatistics.nBadAlignments));
logger.info(String.format(" -> %d reads with indels", TraversalStatistics.nSkippedIndels));
@ -490,6 +491,10 @@ public abstract class TraversalEngine {
TraversalStatistics.nBadAlignments++;
result = true;
why = "No alignment start";
} else if (rec.getDuplicateReadFlag()) {
TraversalStatistics.nDuplicates++;
result = true;
why = "Duplicate reads";
}
else {
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 nBadAlignments;
public static int nSkippedIndels;
public static int nDuplicates;
static {
reset();
@ -32,5 +33,6 @@ public class TraversalStatistics {
nNotPrimary = 0;
nBadAlignments = 0;
nSkippedIndels = 0;
nDuplicates = 0;
}
}