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Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Ryan Poplin 2012-05-30 15:21:35 -04:00
parent 9be4f6894c d09b8d5584
commit 421d0d1435
2 changed files with 4 additions and 3 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java
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@ -102,10 +102,10 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
private int maximumCoverage = 700;
@Argument(fullName = "minimum_median_depth", shortName = "med", doc = "The minimum allowable median coverage, used for calling LOW_MEDIAN_DEPTH", required = false)
private int minMedianDepth = 20;
private int minMedianDepth = 10;
@Argument(fullName = "maximum_insert_size", shortName = "ins", doc = "The maximum allowed distance between a read and its mate", required = false)
private int maxInsertSize = 50;
private int maxInsertSize = 500;
@Argument(fullName = "voting_status_threshold", shortName = "stV", doc = "The needed percentage of samples containing a call for the interval to adopt the call ", required = false)
private double votePercentage = 0.50;

3
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
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@ -37,7 +37,8 @@ public class UnifiedArgumentCollection {
/**
* Controls the model used to calculate the probability that a site is variant plus the various sample genotypes in the data at a given locus.
*/
@Argument(fullName = "p_nonref_model", shortName = "pnrm", doc = "Non-reference probability calculation model to employ -- EXACT is the default option, while GRID_SEARCH is also available.", required = false)
@Advanced
@Argument(fullName = "p_nonref_model", shortName = "pnrm", doc = "Non-reference probability calculation model to employ", required = false)
protected AlleleFrequencyCalculationModel.Model AFmodel = AlleleFrequencyCalculationModel.Model.EXACT;
/**