def run(self, infile, outfile, params):
if not os.path.exists(params.reference_bam):
raise OSError("reference bam file {} does not exist".format(
params.reference_bam))
tmpdir = P.get_temp_dir(clear=True)
statement = (
"mkdir {tmpdir}; "
"samtools sort -n {infile} > {tmpdir}/comp.bam; "
"samtools sort -n {params.reference_bam} > {tmpdir}/ref.bam; "
"{params.path} bam-compare-alignments "
"--output-filename-pattern={outfile}.daisy_bam_compare_alignments_%%s.tsv "
"{params.options} "
"--input-bam={tmpdir}/comp.bam "
"--reference-bam={tmpdir}/ref.bam "
">& {outfile}; "
"rm -rf {tmpdir}; ".format(**locals()))
retval = P.run(statement)
return retval
def run(self, infiles, outfile, params):
tmpdir = P.get_temp_dir(clear=True)
statements = ["mkdir {}".format(tmpdir)]
if params.remove_fields:
cleanup_statement = ("| {params.path} annotate "
"-x {params.remove_fields} "
"2> {outfile}_annotate.log ".format(
**locals()))
else:
cleanup_statement = ""
# the current pattern is properly overly specific and
# substitutes ./. with 0/0
if params.set_missing_genotype_to_reference:
set_genotype = "| perl -p -e 's/\.\/\./0\/0/g'"
else:
set_genotype = ""
with IOTools.open_file(outfile + ".filelist_blocks", "w") as blockf:
for start in range(0, len(infiles), self.block_size):
fn = outfile + ".filelist_{}".format(start)
fn_vcf = os.path.join(tmpdir, "block_{}.vcf.gz".format(start))
with IOTools.open_file(fn, "w") as outf:
end = start + self.block_size
outf.write("\n".join(infiles[start:end]) + "\n")
statements.append("{params.path} merge "
"{params.options} "
"-O v "
"--file-list {outfile}.filelist_{start} "
"2> {outfile}_merge_{start}.log "
"{cleanup_statement} "
"{set_genotype} "
"| bgzip "
"> {fn_vcf}; "
"tabix -p vcf {fn_vcf}".format(**locals()))
blockf.write(fn_vcf + "\n")
if params.restrict_to_all:
filter_statement = ("| {params.path} filter "
"--include \"FORMAT/GT != '.'\" "
"-O v "
"2> {outfile}_filter.log ".format(**locals()))
else:
filter_statement = ""
statements.append("{params.path} merge "
"{params.options} "
"-O v "
"--file-list {outfile}.filelist_blocks "
"2> {outfile}_merge.log "
"{filter_statement} "
"| bgzip "
"> {outfile}; "
"tabix -p vcf {outfile} ".format(**locals()))
statements.append("rm -rf {}".format(tmpdir))
statement = "; ".join(statements)
retvals = P.run(statement, **params._asdict())
return retvals