def collect_bed_regions(filename): regions = [] for record in read_bed_file(filename): if len(record) < 4: record.name = "%s*" % (record.contig, ) regions.append(record) return regions
def collect_bed_regions(filename): regions = [] for record in read_bed_file(filename): if len(record) < 4: record.name = "%s*" % (record.contig,) regions.append(record) return regions
def collect_regions(bedfile, bam_input_handle): """Returns the regions to be genotyped / pileup'd, as a list of bed-regions in the form (contig, start, end), where start is zero-based, and end is open based. """ if bedfile is not None: regions = list(read_bed_file(bedfile)) sort_bed_by_bamfile(bam_input_handle, regions) regions = merge_bed_regions(regions) else: regions = [] for (name, length) in zip(bam_input_handle.references, bam_input_handle.lengths): regions.append((name, 0, length)) return regions