zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Checked for consistency with the previous integration tests, and updated the walker and test to use the new I/O system (always prints 4 digits on floats. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5433 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2011-03-13 15:24:22 +00:00
parent b99e27bf9b
commit 3e3ec85807
2 changed files with 4 additions and 14 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

16
java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java
View File

@ -73,11 +73,6 @@ public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
@Argument(doc="VQSqual key", shortName = "vqskey", required=false)
protected String VQSLOD_KEY = "VQSqual";
@Hidden
@Argument(doc="REMOVE ME", shortName = "rcwpio", required=false)
private static final boolean REMAIN_COMPATIBLE_WITH_PREVIOUS_IO = false;
// @Hidden
// @Argument(doc="Include filtered records", shortName = "ifr", fullName = "IncludeFilteredRecords", required=false)
// protected boolean includeFilteredRecords = false;
@ -275,14 +270,9 @@ public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
double[] normalizedLikelihoods = MathUtils.normalizeFromLog10(log10Likelihoods);
// see if we need to randomly mask out genotype in this position.
// todo -- remove me after testing
if ( REMAIN_COMPATIBLE_WITH_PREVIOUS_IO && (log10Likelihoods == HAPLOID_FLAT_LOG10_LIKELIHOODS || log10Likelihoods == DIPLOID_FLAT_LOG10_LIKELIHOODS) )
for (double likeVal: normalizedLikelihoods)
out.append(String.format("%.2f ",likeVal));
else
for (double likeVal: normalizedLikelihoods) {
out.append(String.format("%5.4f ",likeVal));
}
for (double likeVal: normalizedLikelihoods) {
out.append(String.format("%5.4f ",likeVal));
}
}

2
java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java
View File

@ -60,7 +60,7 @@ public class BeagleIntegrationTest extends WalkerTest {
"-T ProduceBeagleInput -B:variant,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/NA12878_HSQ_chr22_14-16m.vcf "+
"-B:validation,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/NA12878_OMNI_chr22_14-16m.vcf "+
"-L 22:14000000-16000000 -o %s -bvcf %s -bs 0.8 -valp 0.98 -R /humgen/1kg/reference/human_g1k_v37.fasta -NO_HEADER ",2,
Arrays.asList("44d28b6b092d5f4c0ae59af442612ea3","223fb977e8db567dcaf632c6ee51f294"));
Arrays.asList("660986891b30cdc937e0f2a3a5743faa","223fb977e8db567dcaf632c6ee51f294"));
executeTest("test BeagleInputWithBootstrap",spec);
}