/**
* Perform filtering on all VCF files for a given workflow. Filtering involves removing lines that
* are not "PASS" or "." Output files will have ".pass-filtered." in their name.
*
* @param workflowName The workflow to PASS filter
* @param parents List of parent jobs.
* @return
*/
private Job passFilterWorkflow(Pipeline workflowName, Job... parents) {
// Job passFilter = this.getWorkflow().createBashJob("pass filter "+workflowName);
PreprocessJobGenerator generator =
new PreprocessJobGenerator(
this.JSONlocation, this.JSONrepoName, this.JSONfolderName, this.JSONfileName);
Job passFilter = generator.passFilterWorkflow(this, workflowName, parents);
return passFilter;
}
/**
* 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;
}
/**
* 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;
}