def _create_genome_regions(data):
    """Create whole genome contigs we want to process, only non-alts.

    Skips problem contigs like HLAs for downstream analysis.
    """
    work_dir = utils.safe_makedir(os.path.join(dd.get_work_dir(data), "coverage", dd.get_sample_name(data)))
    variant_regions = os.path.join(work_dir, "target-genome.bed")
    with file_transaction(data, variant_regions) as tx_variant_regions:
        with open(tx_variant_regions, "w") as out_handle:
            for c in shared.get_noalt_contigs(data):
                out_handle.write("%s\t%s\t%s\n" % (c.name, 0, c.size))
    return variant_regions
def _create_genome_regions ( data ) : work_dir = utils . safe_makedir ( os . path . join ( dd . get_work_dir ( data ) , "coverage" , dd . get_sample_name ( data ) ) ) variant_regions = os . path . join ( work_dir , "target-genome.bed" ) with file_transaction ( data , variant_regions ) as tx_variant_regions : with open ( tx_variant_regions , "w" ) as out_handle : for c in shared . get_noalt_contigs ( data ) : out_handle . write ( "%s\t%s\t%s\n" % ( c . name , 0 , c . size ) ) return variant_regions
Create whole genome contigs we want to process, only non-alts.

    Skips problem contigs like HLAs for downstream analysis.