/**
* Pre-processes INDEL VCFs. Normalizes INDELs and extracts SNVs from normalized INDELs.
*
* @param parent
* @param workflowName The name of the workflow whose files will be pre-processed.
* @param vcfName The name of the INDEL VCF to normalize.
* @return
*/
private Job preProcessIndelVCF(
Job parent, Pipeline workflowName, String vcfName, String tumourAliquotID) {
PreprocessJobGenerator generator =
new PreprocessJobGenerator(
this.JSONlocation, this.JSONrepo, this.JSONfolderName, this.JSONfileName);
generator.setTumourAliquotID(tumourAliquotID);
Consumer<VcfInfo> updateExtractedSNVs = (v) -> this.extractedSnvsFromIndels.add(v);
Consumer<VcfInfo> updateNormalizedINDELs = (v) -> this.normalizedIndels.add(v);
Job preProcess =
generator.preProcessIndelVCF(
this,
parent,
workflowName,
vcfName,
this.refFile,
this.updateFilesForUpload,
updateExtractedSNVs,
updateNormalizedINDELs);
return preProcess;
}
