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Added a more robust check for Jishu -- am pretty sure the .bam header is busticated 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4223 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-09-08 01:11:22 +00:00
parent ae3f7026a4
commit 71046e650e
1 changed files with 20 additions and 4 deletions
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24
java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
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@ -38,6 +38,7 @@ import org.broadinstitute.sting.gatk.refdata.utils.*;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.commandline.Argument;
@ -283,10 +284,14 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<DoCOutputType.Partiti
}
for(DoCOutputType.Partition partition: partitionTypes) {
printIntervalStats(statsByInterval,
getCorrectStream(partition, DoCOutputType.Aggregation.interval, DoCOutputType.FileType.summary),
getCorrectStream(partition, DoCOutputType.Aggregation.interval, DoCOutputType.FileType.statistics),
partition);
if ( checkType(statsByInterval.get(0).getSecond().getCoverageByAggregationType(partition) ,partition) ) {
printIntervalStats(statsByInterval,
getCorrectStream(partition, DoCOutputType.Aggregation.interval, DoCOutputType.FileType.summary),
getCorrectStream(partition, DoCOutputType.Aggregation.interval, DoCOutputType.FileType.statistics),
partition);
} else {
throw new StingException("Partition type "+partition.toString()+" had no entries. Please check that your .bam header has all appropriate partition types.");
}
}
onTraversalDone(mergeAll(statsByInterval));
@ -769,6 +774,16 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<DoCOutputType.Partiti
}
}
public boolean checkType(DepthOfCoverageStats stats, DoCOutputType.Partition type ) {
if ( stats.getHistograms().size() < 1 ) {
Utils.warnUser("The histogram per partition type "+type.toString()+" was empty\n"+
"Do your read groups have this type? (Check your .bam header).");
return false;
} else {
return true;
}
}
}
class DoCOutputMultiplexer implements Multiplexer<DoCOutputType> {
@ -838,6 +853,7 @@ class DoCOutputMultiplexer implements Multiplexer<DoCOutputType> {
public String transformArgument(final DoCOutputType outputType, final String argument) {
return outputType.getFileName(argument);
}
}
class CoveragePartitioner {