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
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
