/**
* Runs the variant program inside the Broad's OxoG container to produce a mini-BAM for a given
* BAM.
*
* @param parent
* @param bamType - The type of BAM file to use. Determines the name of the output file.
* @param bamPath - The path to the input BAM file.
* @param tumourBAMFileName - Name of the BAM file. Only used if bamType == BAMType.tumour.
* @param aliquotID
* @return
*/
private Job doVariantBam(
BAMType bamType, String bamPath, String tumourBAMFileName, String aliquotID, Job... parents) {
Job runVariantbam;
if (!this.skipVariantBam) {
VariantBamJobGenerator variantBamJobGenerator =
new VariantBamJobGenerator(
this.JSONlocation, this.JSONrepoName, this.JSONfolderName, this.JSONfileName);
variantBamJobGenerator.setGitMoveTestMode(this.gitMoveTestMode);
variantBamJobGenerator.setIndelPadding(String.valueOf(this.indelPadding));
variantBamJobGenerator.setSnvPadding(String.valueOf(this.snvPadding));
variantBamJobGenerator.setSvPadding(String.valueOf(this.svPadding));
variantBamJobGenerator.setGitMoveTestMode(this.gitMoveTestMode);
variantBamJobGenerator.setAliquotID(aliquotID);
variantBamJobGenerator.setSnvVcf(
mergedVcfs.stream().filter(isSnv).findFirst().get().getFileName());
variantBamJobGenerator.setSvVcf(
mergedVcfs.stream().filter(isSv).findFirst().get().getFileName());
variantBamJobGenerator.setIndelVcf(
mergedVcfs.stream().filter(isIndel).findFirst().get().getFileName());
UpdateBamForUpload<String, String, Boolean> updateFilesForUpload =
(path, id, isLink) -> {
if (id == null || id.trim().equals("")) {
// only update the normalMinibamPath with the path to the actual BAM.
// If you get a .bai file here, add it to filesForUpload,
// but don't do anything else.
// Also, if what was passed in has been indicated as a symlink, just add
// to filesForUpload but do nothing else.
if (path.endsWith(".bam") && !isLink) {
this.normalMinibamPath = path;
}
this.filesForUpload.add(path);
} else {
for (TumourInfo tInfo : this.tumours) {
if (tInfo.getAliquotID().equals(id)) {
// Set the tumour minibam path only to the BAM file.
// If you get a .bai file here, add it to filesForUpload,
// but don't do anything else.
// Also, if what was passed in has been indicated as a symlink, just add
// to filesForUpload but do nothing else.
if (path.endsWith(".bam") && !isLink) {
tInfo.setTumourMinibamPath(path);
}
filesForUpload.add(path);
}
}
}
};
String bamName = (bamType == BAMType.normal ? this.normalBAMFileName : tumourBAMFileName);
runVariantbam =
variantBamJobGenerator.doVariantBam(
this, bamType, bamName, bamPath, tumourBAMFileName, updateFilesForUpload, parents);
} else {
runVariantbam =
this.getWorkflow()
.createBashJob(
"run "
+ bamType
+ (bamType == BAMType.tumour ? "_" + aliquotID + "_" : "")
+ " variantbam");
Arrays.stream(parents).forEach(parent -> runVariantbam.addParent(parent));
}
return runVariantbam;
}
