INNER CODE UNIT · Python
proc_chr
nloyfer/wgbs_tools · src/python/bam2pat.py:144
def proc_chr(bam, out_path, region, genome, paired_end, ex_flags, in_flags, top_only, bottom_only,
rg, mapq, debug, blueprint, clip, temp_dir, blacklist, whitelist, min_cpg, mbias, nanopore,
np_thresh, verbose, long, cpc_call='C', combine_mods=False):
""" Convert a temp single chromosome file, extracted from a bam file, into pat """
# Run patter tool on a single chromosome (or region). out_path will have the following fields:
# chr CpG Pattern begin_loc length(bp)
# use samtools to extract only the reads from 'chrom'
if in_flags is None:
in_flags = '-f 3' if paired_end else ''
else:
in_flags = f'-f {in_flags}'
if top_only:
if paired_end:
in_flags += " | awk '($2 == 147 || $2 == 99)' "