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Moved some HC parameters related to active region extensions to command line arguments so that they're more easily modified. Some of these parameters need tinkering in order to call some large indels. See GSA-891 and subtasks for particular examples thereof.

This commit is contained in:
Guillermo del Angel 2013-07-10 14:29:13 -04:00
parent 2d81234ed8
commit aba55dbb23
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