/**
* Does all annotations for the workflow.
*
* @param parents
* @return
*/
private List<Job> doAnnotations(Job... parents) {
List<Job> finalAnnotatorJobs = new ArrayList<Job>();
Predicate<String> isExtractedSNV = p -> p.contains("extracted-snv") && p.endsWith(".vcf.gz");
final String passFilteredOxoGSuffix = ".pass-filtered.oxoG.vcf.gz";
// list filtering should only ever produce one result.
for (int i = 0; i < this.tumours.size(); i++) {
TumourInfo tInf = this.tumours.get(i);
String tumourAliquotID = tInf.getAliquotID();
PcawgAnnotatorJobGenerator generator =
new PcawgAnnotatorJobGenerator(
this.JSONlocation, this.JSONrepoName, this.JSONfolderName, this.JSONfileName);
generator.setGitMoveTestMode(this.gitMoveTestMode);
generator.setAllowMissingFiles(this.allowMissingFiles);
generator.setBroadOxogSNVFileName(
this.filesForUpload
.stream()
.filter(
p ->
((p.contains(tumourAliquotID)
&& p.contains("broad-mutect")
&& p.endsWith(passFilteredOxoGSuffix))))
.findFirst()
.orElseGet(emptyStringWhenMissingFilesAllowed));
generator.setBroadOxoGSNVFromIndelFileName(
this.filesForUpload
.stream()
.filter(p -> (p.contains(Pipeline.broad.toString()) && isExtractedSNV.test(p)))
.findFirst()
.orElseGet(emptyStringWhenMissingFilesAllowed));
generator.setSangerOxogSNVFileName(
this.filesForUpload
.stream()
.filter(
p ->
((p.contains(tumourAliquotID)
&& p.contains("svcp_")
&& p.endsWith(passFilteredOxoGSuffix))))
.findFirst()
.orElseGet(emptyStringWhenMissingFilesAllowed));
generator.setSangerOxoGSNVFromIndelFileName(
this.filesForUpload
.stream()
.filter(p -> (p.contains(Pipeline.sanger.toString()) && isExtractedSNV.test(p)))
.findFirst()
.orElseGet(emptyStringWhenMissingFilesAllowed));
generator.setDkfzEmbleOxogSNVFileName(
this.filesForUpload
.stream()
.filter(
p ->
((p.contains(tumourAliquotID)
&& p.contains("dkfz-snvCalling")
&& p.endsWith(passFilteredOxoGSuffix))))
.findFirst()
.orElseGet(emptyStringWhenMissingFilesAllowed));
generator.setDkfzEmblOxoGSNVFromIndelFileName(
this.filesForUpload
.stream()
.filter(p -> (p.contains(Pipeline.dkfz_embl.toString()) && isExtractedSNV.test(p)))
.findFirst()
.orElseGet(emptyStringWhenMissingFilesAllowed));
// Remember: MUSE files do not get PASS-filtered. Also, there is no INDEL so there cannot be
// any SNVs extracted from INDELs.
generator.setMuseOxogSNVFileName(
this.filesForUpload
.stream()
.filter(p -> p.toUpperCase().contains("MUSE") && p.endsWith(".oxoG.vcf.gz"))
.findFirst()
.orElseGet(emptyStringWhenMissingFilesAllowed));
generator.setNormalizedBroadIndel(
this.normalizedIndels
.stream()
.filter(CommonPredicates.isBroad.and(matchesTumour(tumourAliquotID)))
.findFirst()
.orElse(new VcfInfo())
.getFileName());
generator.setNormalizedDkfzEmblIndel(
this.normalizedIndels
.stream()
.filter(CommonPredicates.isDkfzEmbl.and(matchesTumour(tumourAliquotID)))
.findFirst()
.orElse(new VcfInfo())
.getFileName());
generator.setNormalizedSangerIndel(
this.normalizedIndels
.stream()
.filter(CommonPredicates.isSanger.and(matchesTumour(tumourAliquotID)))
.findFirst()
.orElse(new VcfInfo())
.getFileName());
List<Job> jobs =
generator.doAnnotations(
this,
tInf.getAliquotID(),
tInf.getTumourMinibamPath(),
this.normalMinibamPath,
this.updateFilesForUpload,
parents);
finalAnnotatorJobs.addAll(jobs);
}
return finalAnnotatorJobs;
}
