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

Merge pull request #690 from broadinstitute/vrr_fix_non_diploid_unsupproted_message_in_haplotype_caller 

Add diploid only support message to HaplotypeCaller
This commit is contained in:
Valentin Ruano Rubio 2014-07-29 22:50:00 -04:00
parent 43bd6b4436 750eb4b5a6
commit d69af637bf
1 changed files with 4 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
View File

@ -95,6 +95,7 @@ import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType;
import htsjdk.variant.variantcontext.*;
import htsjdk.variant.variantcontext.writer.VariantContextWriter;
import htsjdk.variant.vcf.*;
import org.broadinstitute.gatk.utils.variant.HomoSapiensConstants;
import java.io.FileNotFoundException;
import java.io.PrintStream;
@ -614,6 +615,9 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
public void initialize() {
super.initialize();
if (SCAC.genotypeArgs.samplePloidy != HomoSapiensConstants.DEFAULT_PLOIDY)
throw new UserException.BadArgumentValue("-ploidy", "" + SCAC.genotypeArgs.samplePloidy + "; currently HaplotypeCaller only supports diploid sample analysis (-ploidy 2)");
if (dontGenotype && emitReferenceConfidence())
throw new UserException("You cannot request gVCF output and do not genotype at the same time");