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Merge pull request #699 from broadinstitute/tf_hc_block_ranges 

Changed the default GVCF Q Bands from 5,20,60 to be 1..60 by 1s, 60...90...
This commit is contained in:
Eric Banks 2014-08-08 16:10:23 -04:00
parent 683baff375 5695f22da8
commit abcaba4bc3
2 changed files with 8 additions and 5 deletions
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5
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
View File

@ -408,7 +408,10 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
*/
@Advanced
@Argument(fullName="GVCFGQBands", shortName="GQB", doc="Emit experimental reference confidence scores", required = false)
protected List<Integer> GVCFGQBands = Arrays.asList(5, 20, 60);
protected List<Integer> GVCFGQBands = new ArrayList<Integer>(70) {{
for (int i=1; i<=60; ++i) add(i);
add(70); add(80); add(90); add(99);
}};
/**
* This parameter determines the maximum size of an indel considered as potentially segregating in the

8
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
View File

@ -69,10 +69,10 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
// this functionality can be adapted to provide input data for whatever you might want in your data
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "9db87ae56df22456f3c08024384f3e5e"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "4a006f9e39cacc3ae84384ad56ca22a2"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "cb048cbfa5cc058d680f9be5fd689767"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "fe014592c9fa8d442508a96eb09e0c93"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "d5c07fa3edca496a84fd17cecad06230"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "330685c734e277d70a44637de85ad54d"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "e6ec90da053a612f0c615e221eb34baa"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "b01a2c222a3f00a675f5534c3b449919"});
return tests.toArray(new Object[][]{});
}
@ -137,7 +137,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
public void testWrongGVCFNonVariantRecordOrderBugFix() {
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
b37KGReference, WRONG_GVCF_RECORD_ORDER_BUGFIX_BAM, WRONG_GVCF_RECORD_ORDER_BUGFIX_INTERVALS, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("9fecd24420579f321157e5605b6cd7f2"));
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("d595dae0e3f993047c22c6e520e190aa"));
spec.disableShadowBCF();
executeTest("testMissingGVCFIndexingStrategyException", spec);
}
@ -149,7 +149,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
public void testNoCallGVCFMissingPLsBugFix() {
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
b37KGReference, NOCALL_GVCF_BUGFIX_BAM, NOCALL_GVCF_BUGFIX_INTERVALS, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("95bae0b4a8fe9bfcf71762704b22a76e"));
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("2a91768430a84dbae8d40242dee8c9b8"));
spec.disableShadowBCF();
executeTest("testNoCallGVCFMissingPLsBugFix", spec);
}