834a4f2701482fc13af9cdf4873ec92941ba853e,cnvlib/commands.py,,batch_run_sample,#Any#Any#Any#Any#Any#Any#Any#Any#Any#Any#,192

Before Change

                     diagram=False, rlibpath=None, by_count=False):
    Run the pipeline on one BAM file.
    // ENH - return probes, segments (cnarr, segarr)
    echo("Running the CNVkit pipeline on", bam_fname, "...")
    sample_id = core.fbase(bam_fname)
    sample_pfx = os.path.join(output_dir, sample_id)

    raw_tgt = do_coverage(target_bed, bam_fname, by_count)

After Change

                     diagram=False, rlibpath=None, by_count=False):
    Run the pipeline on one BAM file.
    // ENH - return probes, segments (cnarr, segarr)
    logging.info("Running the CNVkit pipeline on %s ...", bam_fname)
    sample_id = core.fbase(bam_fname)
    sample_pfx = os.path.join(output_dir, sample_id)

    raw_tgt = do_coverage(target_bed, bam_fname, by_count)
    raw_tgt.write(sample_pfx + ".targetcoverage.cnn")

    raw_anti = do_coverage(antitarget_bed, bam_fname, by_count)
    raw_anti.write(sample_pfx + ".antitargetcoverage.cnn")

    cnarr = do_fix(raw_tgt, raw_anti, _CNA.read(ref_fname))
    cnarr.write(sample_pfx + ".cnr")

    logging.info("Segmenting %s.cnr ...", sample_pfx)
    segments = segmentation.do_segmentation(cnarr, "cbs", rlibpath=rlibpath)
    segments.write(sample_pfx + ".cns")

    if scatter:
        do_scatter(cnarr, segments)
        pyplot.savefig(sample_pfx + "-scatter.pdf", format="pdf",
                       bbox_inches="tight")
        logging.info("Wrote %s-scatter.pdf", sample_pfx)

    if diagram:
        from cnvlib import diagram
        outfname = sample_pfx + "-diagram.pdf"

Instances