/**
* Combine vcfs by from from ALL tumours. This is needed when generating the minibam for Normals
* BAMs in a multi-tumour scenario.
*
* @param parents
* @return
*/
private Job combineVCFsByType(Job... parents) {
PreprocessJobGenerator generator =
new PreprocessJobGenerator(
this.JSONlocation, this.JSONrepo, this.JSONfolderName, this.JSONfileName);
List<VcfInfo> nonIndels =
this.vcfs.stream().filter(p -> isIndel.negate().test(p)).collect(Collectors.toList());
List<VcfInfo> indels = this.normalizedIndels.stream().collect(Collectors.toList());
Consumer<VcfInfo> updateMergedVCFs = (v) -> this.mergedVcfs.add(v);
Job vcfCombineJob =
generator.combineVCFsByType(this, nonIndels, indels, updateMergedVCFs, parents);
return vcfCombineJob;
}
