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A temporary @hidden hack to get indel calling done for Phase I: don't try to call if there's too much coverage. Do not use this unless your last name rhymes with Shmoplin. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5348 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-03-01 19:22:27 +00:00
parent 8ab6eee1cf
commit a20ce1436d
2 changed files with 10 additions and 0 deletions
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7
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
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@ -65,6 +65,11 @@ public class UnifiedArgumentCollection {
@Argument(fullName = "assume_single_sample_reads", shortName = "single_sample", doc = "The single sample that we should assume is represented in the input bam (and therefore associate with all reads regardless of whether they have read groups)", required = false)
public String ASSUME_SINGLE_SAMPLE = null;
// TODO -- delete me
@Hidden
@Argument(fullName = "abort_at_too_much_coverage", doc = "Don't call a site if the downsampled coverage is greater than this value", required = false)
public int COVERAGE_AT_WHICH_TO_ABORT = -1;
// control the various parameters to be used
@Argument(fullName = "min_base_quality_score", shortName = "mbq", doc = "Minimum base quality required to consider a base for calling", required = false)
@ -135,6 +140,8 @@ public class UnifiedArgumentCollection {
uac.ALPHA_DELETION_PROBABILITY = ALPHA_DELETION_PROBABILITY;
uac.EXACT_CALCULATION_TYPE = EXACT_CALCULATION_TYPE;
uac.COVERAGE_AT_WHICH_TO_ABORT = COVERAGE_AT_WHICH_TO_ABORT;
return uac;
}

3
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -157,6 +157,9 @@ public class UnifiedGenotyperEngine {
* @return the VariantCallContext object
*/
public VariantCallContext calculateLikelihoodsAndGenotypes(RefMetaDataTracker tracker, ReferenceContext refContext, AlignmentContext rawContext) {
if ( UAC.COVERAGE_AT_WHICH_TO_ABORT > 0 && rawContext.size() > UAC.COVERAGE_AT_WHICH_TO_ABORT )
return null;
Map<String, StratifiedAlignmentContext> stratifiedContexts = getFilteredAndStratifiedContexts(UAC, refContext, rawContext);
if ( stratifiedContexts == null )
return (UAC.OutputMode != OUTPUT_MODE.EMIT_ALL_SITES ? null : new VariantCallContext(generateEmptyContext(tracker, refContext, stratifiedContexts, rawContext), refContext.getBase(), false));