Examples with ModeledSegment org.broadinstitute.hellbender.tools.exome.ModeledSegment used on opensource projects

Example 16 with ModeledSegment

use of org.broadinstitute.hellbender.tools.exome.ModeledSegment in project gatk-protected by broadinstitute.

the class PerformCopyRatioSegmentation method doWork.

@Override
public Object doWork() {
    final String sampleName = ReadCountCollectionUtils.getSampleNameForCLIsFromReadCountsFile(new File(coverageFile));
    final ReadCountCollection rcc;
    try {
        rcc = ReadCountCollectionUtils.parse(new File(coverageFile));
    } catch (final IOException ex) {
        throw new UserException.BadInput("could not read input file");
    }
    final CopyRatioSegmenter segmenter = new CopyRatioSegmenter(initialNumStates, rcc);
    final List<ModeledSegment> segments = segmenter.getModeledSegments();
    SegmentUtils.writeModeledSegmentFile(outputSegmentsFile, segments, sampleName, false);
    return "SUCCESS";
}