Examples with PartialAlignmentsAssemblerParameters com.milaboratory.mixcr.partialassembler.PartialAlignmentsAssemblerParameters used on opensource projects

Example 1 with PartialAlignmentsAssemblerParameters

use of com.milaboratory.mixcr.partialassembler.PartialAlignmentsAssemblerParameters in project mixcr by milaboratory.

the class ActionAssemblePartialAlignments method go.

@Override
public void go(ActionHelper helper) throws Exception {
    if (parameters.writePartial != null)
        System.err.println("'-p' option is deprecated and will be removed in 2.2. " + "Use '-d' option to drop not-overlapped partial reads.");
    // Saving initial timestamp
    long beginTimestamp = System.currentTimeMillis();
    PartialAlignmentsAssemblerParameters assemblerParameters = PartialAlignmentsAssemblerParameters.getDefault();
    if (!parameters.overrides.isEmpty()) {
        assemblerParameters = JsonOverrider.override(assemblerParameters, PartialAlignmentsAssemblerParameters.class, parameters.overrides);
        if (assemblerParameters == null) {
            System.err.println("Failed to override some parameter.");
            return;
        }
    }
    try (PartialAlignmentsAssembler assembler = new PartialAlignmentsAssembler(assemblerParameters, parameters.getOutputFileName(), !parameters.doDropPartial(), parameters.getOverlappedOnly())) {
        ReportWrapper report = new ReportWrapper(command(), assembler);
        report.setStartMillis(beginTimestamp);
        report.setInputFiles(parameters.getInputFileName());
        report.setOutputFiles(parameters.getOutputFileName());
        report.setCommandLine(helper.getCommandLineArguments());
        try (VDJCAlignmentsReader reader = new VDJCAlignmentsReader(parameters.getInputFileName())) {
            SmartProgressReporter.startProgressReport("Building index", reader);
            assembler.buildLeftPartsIndex(reader);
        }
        try (VDJCAlignmentsReader reader = new VDJCAlignmentsReader(parameters.getInputFileName())) {
            SmartProgressReporter.startProgressReport("Searching for overlaps", reader);
            assembler.searchOverlaps(reader);
        }
        report.setFinishMillis(System.currentTimeMillis());
        // Writing report to stout
        System.out.println("============= Report ==============");
        Util.writeReportToStdout(report);
        if (parameters.report != null)
            Util.writeReport(parameters.report, report);
        if (parameters.jsonReport != null)
            Util.writeJsonReport(parameters.jsonReport, report);
    }
}