use of com.milaboratory.core.PairedEndReadsLayout in project mixcr by milaboratory.
the class ActionAlign method go.
@Override
@SuppressWarnings("unchecked")
public void go(ActionHelper helper) throws Exception {
// FIXME remove in 2.2
if (actionParameters.printNonFunctionalWarnings())
System.out.println("WARNING: -wf / --non-functional-warnings option is deprecated, will be removed in 2.2 " + "release. Use --verbose instead.");
// Saving initial timestamp
long beginTimestamp = System.currentTimeMillis();
// Getting aligner parameters
VDJCAlignerParameters alignerParameters = actionParameters.getAlignerParameters();
// FIXME remove in 2.3
if (actionParameters.getSaveOriginalReads()) {
System.out.println("WARNING: -g / --save-reads option is deprecated, will be removed in 2.3 " + "release. Use -OsaveOriginalReads=true.");
alignerParameters.setSaveOriginalReads(true);
}
// FIXME remove in 2.3
if (actionParameters.getSaveReadDescription()) {
System.out.println("WARNING: -a / --save-description option is deprecated, will be removed in 2.3 " + "release. Use -OsaveOriginalReads=true.");
alignerParameters.setSaveOriginalReads(true);
}
if (!actionParameters.overrides.isEmpty()) {
// Perform parameters overriding
alignerParameters = JsonOverrider.override(alignerParameters, VDJCAlignerParameters.class, actionParameters.overrides);
if (alignerParameters == null)
throw new ProcessException("Failed to override some parameter.");
}
// FIXME remove in 2.2
if (actionParameters.allowDifferentVJLoci != null && actionParameters.allowDifferentVJLoci) {
System.out.println("Warning: usage of --diff-loci is deprecated. Use -OallowChimeras=true instead.");
alignerParameters.setAllowChimeras(true);
}
// Creating aligner
VDJCAligner aligner = VDJCAligner.createAligner(alignerParameters, actionParameters.isInputPaired(), !actionParameters.getNoMerge());
// Detect if automatic featureToAlign correction is required
int totalV = 0, totalVErrors = 0, hasVRegion = 0;
GeneFeature correctingFeature = alignerParameters.getVAlignerParameters().getGeneFeatureToAlign().hasReversedRegions() ? GeneFeature.VRegionWithP : GeneFeature.VRegion;
VDJCLibrary library = VDJCLibraryRegistry.getDefault().getLibrary(actionParameters.library, actionParameters.species);
System.out.println("Reference library: " + library.getLibraryId());
// Printing library level warnings, if specified for the library
if (!library.getWarnings().isEmpty()) {
System.out.println("Library warnings:");
for (String l : library.getWarnings()) System.out.println(l);
}
// Printing citation notice, if specified for the library
if (!library.getCitations().isEmpty()) {
System.out.println("Please cite:");
for (String l : library.getCitations()) System.out.println(l);
}
for (VDJCGene gene : library.getGenes(actionParameters.getChains())) {
if (gene.getGeneType() == GeneType.Variable) {
totalV++;
if (!alignerParameters.containsRequiredFeature(gene)) {
totalVErrors++;
if (gene.getPartitioning().isAvailable(correctingFeature))
hasVRegion++;
}
}
}
// Performing V featureToAlign correction if needed
if (totalVErrors > totalV * 0.9 && hasVRegion > totalVErrors * 0.8) {
System.out.println("WARNING: forcing -OvParameters.geneFeatureToAlign=" + GeneFeature.encode(correctingFeature) + " since current gene feature (" + GeneFeature.encode(alignerParameters.getVAlignerParameters().getGeneFeatureToAlign()) + ") is absent in " + Util.PERCENT_FORMAT.format(100.0 * totalVErrors / totalV) + "% of V genes.");
alignerParameters.getVAlignerParameters().setGeneFeatureToAlign(correctingFeature);
}
int numberOfExcludedNFGenes = 0;
int numberOfExcludedFGenes = 0;
for (VDJCGene gene : library.getGenes(actionParameters.getChains())) {
NucleotideSequence featureSequence = alignerParameters.extractFeatureToAlign(gene);
// exclusionReason is null ==> gene is not excluded
String exclusionReason = null;
if (featureSequence == null)
exclusionReason = "absent " + GeneFeature.encode(alignerParameters.getFeatureToAlign(gene.getGeneType()));
else if (featureSequence.containsWildcards())
exclusionReason = "wildcard symbols in " + GeneFeature.encode(alignerParameters.getFeatureToAlign(gene.getGeneType()));
if (exclusionReason == null)
// If there are no reasons to exclude the gene, adding it to aligner
aligner.addGene(gene);
else {
if (gene.isFunctional()) {
++numberOfExcludedFGenes;
if (actionParameters.verbose())
System.out.println("WARNING: Functional gene " + gene.getName() + " excluded due to " + exclusionReason);
} else
++numberOfExcludedNFGenes;
}
}
if (actionParameters.printWarnings() && numberOfExcludedFGenes > 0)
System.out.println("WARNING: " + numberOfExcludedFGenes + " functional genes were excluded, re-run " + "with --verbose option to see the list of excluded genes and exclusion reason.");
if (actionParameters.verbose() && numberOfExcludedNFGenes > 0)
System.out.println("WARNING: " + numberOfExcludedNFGenes + " non-functional genes excluded.");
if (aligner.getVGenesToAlign().isEmpty())
throw new ProcessException("No V genes to align. Aborting execution. See warnings for more info " + "(turn on verbose warnings by adding --verbose option).");
if (aligner.getJGenesToAlign().isEmpty())
throw new ProcessException("No J genes to align. Aborting execution. See warnings for more info " + "(turn on verbose warnings by adding --verbose option).");
AlignerReport report = new AlignerReport();
report.setStartMillis(beginTimestamp);
report.setInputFiles(actionParameters.getInputsForReport());
report.setOutputFiles(actionParameters.getOutputsForReport());
report.setCommandLine(helper.getCommandLineArguments());
// Attaching report to aligner
aligner.setEventsListener(report);
try (SequenceReaderCloseable<? extends SequenceRead> reader = actionParameters.createReader();
VDJCAlignmentsWriter writer = actionParameters.getOutputName().equals(".") ? null : new VDJCAlignmentsWriter(actionParameters.getOutputName());
SequenceWriter notAlignedWriter = actionParameters.failedReadsR1 == null ? null : (actionParameters.isInputPaired() ? new PairedFastqWriter(actionParameters.failedReadsR1, actionParameters.failedReadsR2) : new SingleFastqWriter(actionParameters.failedReadsR1))) {
if (writer != null)
writer.header(aligner);
OutputPort<? extends SequenceRead> sReads = reader;
CanReportProgress progress = (CanReportProgress) reader;
if (actionParameters.limit != 0) {
sReads = new CountLimitingOutputPort<>(sReads, actionParameters.limit);
progress = SmartProgressReporter.extractProgress((CountLimitingOutputPort<?>) sReads);
}
final boolean writeAllResults = actionParameters.getWriteAllResults();
EnumMap<GeneType, VDJCHit[]> emptyHits = new EnumMap<>(GeneType.class);
for (GeneType gt : GeneType.values()) if (alignerParameters.getGeneAlignerParameters(gt) != null)
emptyHits.put(gt, new VDJCHit[0]);
final PairedEndReadsLayout readsLayout = alignerParameters.getReadsLayout();
SmartProgressReporter.startProgressReport("Alignment", progress);
OutputPort<Chunk<? extends SequenceRead>> mainInputReads = CUtils.buffered((OutputPort) chunked(sReads, 64), 16);
OutputPort<VDJCAlignmentResult> alignments = unchunked(new ParallelProcessor(mainInputReads, chunked(aligner), actionParameters.threads));
for (VDJCAlignmentResult result : CUtils.it(new OrderedOutputPort<>(alignments, new Indexer<VDJCAlignmentResult>() {
@Override
public long getIndex(VDJCAlignmentResult o) {
return o.read.getId();
}
}))) {
VDJCAlignments alignment = result.alignment;
SequenceRead read = result.read;
if (alignment == null) {
if (writeAllResults) // Creating empty alignment object if alignment for current read failed
{
Target target = readsLayout.createTargets(read)[0];
alignment = new VDJCAlignments(emptyHits, target.targets, SequenceHistory.RawSequence.of(read.getId(), target), alignerParameters.isSaveOriginalReads() ? new SequenceRead[] { read } : null);
} else {
if (notAlignedWriter != null)
notAlignedWriter.write(result.read);
continue;
}
}
if (alignment.isChimera())
report.onChimera();
if (writer != null)
writer.write(alignment);
}
if (writer != null)
writer.setNumberOfProcessedReads(reader.getNumberOfReads());
}
report.setFinishMillis(System.currentTimeMillis());
// Writing report to stout
System.out.println("============= Report ==============");
Util.writeReportToStdout(report);
if (actionParameters.report != null)
Util.writeReport(actionParameters.report, report);
if (actionParameters.jsonReport != null)
Util.writeJsonReport(actionParameters.jsonReport, report);
}
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