def split(args):
vc_mode, variant_caller, precalled_filename, gatk_path = tk_io.get_vc_mode(
args.vc_precalled, args.variant_mode)
precalled_file = None
if vc_mode == "precalled" or vc_mode == "precalled_plus":
mem_gb = 8
threads = 1
precalled_file = martian.make_path("precalled_vcf.vcf")
tenkit.log_subprocess.check_call(
['cp', precalled_filename, precalled_file])
tk_tabix.index_vcf(precalled_file)
precalled_file = precalled_file + ".gz"
if vc_mode != "precalled":
if variant_caller == 'freebayes':
mem_gb = 5
threads = 1
elif variant_caller == "gatk":
mem_gb = 8
threads = 2
# make sure the gatk jar file exists
if gatk_path is None:
martian.throw(
"variant_caller 'gatk' selected, must supply path to gatk jar file -- e.g. \"gatk:/path/to/GenomeAnalysisTK.jar\""
)
gatk_loc = gatk_path
if not (os.path.exists(gatk_loc)):
martian.throw(
"variant_caller 'gatk' selected, gatk jar file does not exist: %s"
% gatk_loc)
else:
raise NotSupportedException('Variant caller not supported: ' +
vc_mode)
primary_contigs = tk_reference.load_primary_contigs(args.reference_path)
bam_chunk_size_gb = 3.0
if args.restrict_locus is None:
loci = tk_chunks.get_sized_bam_chunks(args.input,
bam_chunk_size_gb,
contig_whitelist=primary_contigs,
extra_args={
'__mem_gb': mem_gb,
'__threads': threads,
'split_input': precalled_file
})
else:
loci = [{'locus': args.restrict_locus}]
return {'chunks': loci}
def combine_vcfs(output_filename, input_vcf_filenames):
tmp_filename = output_filename + ".tmp"
for (i, fn) in enumerate(input_vcf_filenames):
if i == 0:
args = 'cat ' + fn
subprocess.check_call(args + " > " + tmp_filename, shell=True)
else:
args = 'grep -v "^#" ' + fn
ret = subprocess.call(args + " >> " + tmp_filename, shell=True)
if ret == 2:
raise Exception("grep call failed: " + args)
# Sort and index the files
tk_tabix.sort_vcf(tmp_filename, output_filename)
tk_tabix.index_vcf(output_filename)
os.remove(tmp_filename)
def join(args, outs, chunk_defs, chunk_outs):
# mapping of cluster ID -> VCFs
to_merge = collections.defaultdict(list)
for o, d in zip(chunk_outs, chunk_defs):
to_merge[d.cluster_id].append(o.variant_subset)
# merge each VCF subset for a cluster
merged_vcfs = []
for cluster_id, vcf_list in to_merge.iteritems():
merged_vcf = martian.make_path('{}.vcf'.format(cluster_id))
tk_io.combine_vcfs(merged_vcf, vcf_list)
merged_vcfs.append(merged_vcf + '.gz')
# final merge to make one combined VCF
tmp = martian.make_path('tmp.vcf')
cmd = ['vcf-merge'] + merged_vcfs
with open(tmp, 'w') as outf:
subprocess.check_call(cmd, stdout=outf)
# Sort and index the files
tk_tabix.sort_vcf(tmp, outs.variants.replace('.gz', ''))
tk_tabix.index_vcf(outs.variants.replace('.gz', ''))
os.remove(tmp)
def main_sort_variants(args, outs):
if args.input is None or args.input == [None]:
outs.default = None
else:
outs.coerce_strings()
# List of inputs
sort_filename = outs.default[0:(len(outs.default)-3)]
if type(args.input) == type([]):
files = [f for f in args.input if os.path.isfile(f)]
if len(files) == 0:
outs.defaut = None
return
cat_filename = outs.default[:-3]
tk_io.combine_vcfs(cat_filename, args.input)
# Single input
else:
if not os.path.exists(args.input):
outs.default = None
return
tk_tabix.sort_vcf(args.input, sort_filename)
tk_tabix.index_vcf(sort_filename)