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Merge pull request #741 from broadinstitute/rhl_activiteregion_read_limits_args 

Changed hardcoded downsampling max/min coverage values to parameters
This commit is contained in:
jmthibault79 2014-10-09 18:49:22 -04:00
parent 1cbf37c539 645d418015
commit 4e099c1f44
2 changed files with 10 additions and 3 deletions
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11
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
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@ -608,8 +608,15 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
// reference base padding size
private static final int REFERENCE_PADDING = 500;
private final static int maxReadsInRegionPerSample = 1000; // TODO -- should be an argument
private final static int minReadsPerAlignmentStart = 5; // TODO -- should be an argument
/**
* When downsampling, level the coverage of the reads in each sample to no more than maxReadsInRegionPerSample reads,
* not reducing coverage at any read start to less than minReadsPerAlignmentStart
*/
@Argument(fullName = "maxReadsInRegionPerSample", shortName = "maxReadsInRegionPerSample", doc="Maximum reads in an active region", required = false)
protected int maxReadsInRegionPerSample = 1000;
@Argument(fullName = "minReadsPerAlignmentStart", shortName = "minReadsPerAlignStart", doc="Minimum number of reads sharing the same alignment start for each genomic location in an active region", required = false)
protected int minReadsPerAlignmentStart = 5;
private byte MIN_TAIL_QUALITY;
private static final byte MIN_TAIL_QUALITY_WITH_ERROR_CORRECTION = 6;

2
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
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@ -78,7 +78,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
final static String GGA_INTERVALS_FILE = privateTestDir + "haplotype-caller-reduced-test-interval.list";
private void HCTest(String bam, String args, String md5) {
final String base = String.format("-T HaplotypeCaller --contamination_fraction_to_filter 0.05 --disableDithering --pcr_indel_model NONE -R %s -I %s -L %s", REF, bam, INTERVALS_FILE) + " --no_cmdline_in_header -o %s -minPruning 3";
final String base = String.format("-T HaplotypeCaller --contamination_fraction_to_filter 0.05 --disableDithering --pcr_indel_model NONE --maxReadsInRegionPerSample 1000 --minReadsPerAlignmentStart 5 -R %s -I %s -L %s", REF, bam, INTERVALS_FILE) + " --no_cmdline_in_header -o %s -minPruning 3";
final WalkerTestSpec spec = new WalkerTestSpec(base + " " + args, Arrays.asList(md5));
executeTest("testHaplotypeCaller: args=" + args, spec);
}