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Merge pull request #327 from broadinstitute/gda_large_indel_improvement 

Moved some HC parameters related to active region extensions to command ...
This commit is contained in:
Eric Banks 2013-07-11 06:58:13 -07:00
parent 2d81234ed8 aba55dbb23
commit ccc0ee5b4d
1 changed files with 21 additions and 8 deletions
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29
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
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@ -466,6 +466,27 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
@Argument(fullName="minObservationsForKmerToBeSolid", shortName="minObservationsForKmerToBeSolid", doc = "A k-mer must be seen at least these times for it considered to be solid", required=false)
protected int minObservationsForKmerToBeSolid = 20;
/**
* the maximum extent into the full active region extension that we're willing to go in genotyping our events
*/
@Hidden
@Argument(fullName="maxDiscARExtension", shortName="maxDiscARExtension", doc = "the maximum extent into the full active region extension that we're willing to go in genotyping our events for discovery", required=false)
protected int MAX_DISCOVERY_ACTIVE_REGION_EXTENSION = 25;
@Hidden
@Argument(fullName="maxGGAARExtension", shortName="maxGGAARExtension", doc = "the maximum extent into the full active region extension that we're willing to go in genotyping our events for GGA mode", required=false)
protected int MAX_GGA_ACTIVE_REGION_EXTENSION = 300;
/**
* Include at least this many bases around an event for calling it
*/
@Hidden
@Argument(fullName="paddingAroundIndels", shortName="paddingAroundIndels", doc = "Include at least this many bases around an event for calling indels", required=false)
protected int PADDING_AROUND_OTHERS_FOR_CALLING = 150;
@Hidden
@Argument(fullName="paddingAroundSNPs", shortName="paddingAroundSNPs", doc = "Include at least this many bases around an event for calling snps", required=false)
protected int PADDING_AROUND_SNPS_FOR_CALLING = 20;
// -----------------------------------------------------------------------------------------------
// done with Haplotype caller parameters
@ -492,14 +513,6 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
// reference base padding size
private static final int REFERENCE_PADDING = 500;
// include at least this many bases around an event for calling it
private final static int PADDING_AROUND_SNPS_FOR_CALLING = 20;
private final static int PADDING_AROUND_OTHERS_FOR_CALLING = 150;
// the maximum extent into the full active region extension that we're willing to go in genotyping our events
private final static int MAX_DISCOVERY_ACTIVE_REGION_EXTENSION = 25;
private final static int MAX_GGA_ACTIVE_REGION_EXTENSION = 100;
private ActiveRegionTrimmer trimmer = null;
private final static int maxReadsInRegionPerSample = 1000; // TODO -- should be an argument