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Merge pull request #442 from broadinstitute/gg_fixdoc_deletions 

Fixed documentation for -deletions argument in the UAC
This commit is contained in:
Eric Banks 2013-12-04 17:37:18 -08:00
parent 0d94019bd6 3ab2f4edb2
commit 623aaa0d6f
1 changed files with 5 additions and 1 deletions
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6
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
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@ -95,7 +95,11 @@ public class UnifiedArgumentCollection extends StandardCallerArgumentCollection
@Argument(fullName = "min_base_quality_score", shortName = "mbq", doc = "Minimum base quality required to consider a base for calling", required = false) @Argument(fullName = "min_base_quality_score", shortName = "mbq", doc = "Minimum base quality required to consider a base for calling", required = false)
public int MIN_BASE_QUALTY_SCORE = 17; public int MIN_BASE_QUALTY_SCORE = 17;
@Argument(fullName = "max_deletion_fraction", shortName = "deletions", doc = "Maximum fraction of reads with deletions spanning this locus for it to be callable [to disable, set to < 0 or > 1; default:0.05]", required = false) /**
* If the fraction of reads with deletions spanning a locus is greater than this value, the site will not be considered callable and will be skipped.
* To disable the use of this parameter, set its value to >1.
*/
@Argument(fullName = "max_deletion_fraction", shortName = "deletions", doc = "Maximum fraction of reads with deletions spanning this locus for it to be callable", required = false)
public Double MAX_DELETION_FRACTION = 0.05; public Double MAX_DELETION_FRACTION = 0.05;
/** /**