def snp_and_indel_bcf(self):
jobs = []
input_bams = [os.path.join("alignment", sample.name, sample.name + ".sorted.dup.recal.bam") for sample in self.samples]
nb_jobs = config.param('snp_and_indel_bcf', 'approxNbJobs', required=False, type='int')
output_directory = "variants/rawBCF"
bcftools_view_options = "-bvcg"
if nb_jobs and nb_jobs > 1:
for region in self.generate_approximate_windows(nb_jobs):
job = pipe_jobs([
samtools.mpileup(input_bams, None, config.param('snp_and_indel_bcf', 'extra_mpileup_options'), region),
samtools.bcftools_view("-", os.path.join(output_directory, "allSamples." + region + ".bcf"), bcftools_view_options),
])
job.name = "snp_and_indel_bcf.allSamples." + re.sub(":", "_", region)
jobs.append(job)
else:
job = pipe_jobs([
samtools.mpileup(input_bams, None, config.param('snp_and_indel_bcf', 'extra_mpileup_options')),
samtools.bcftools_view("-", os.path.join(output_directory, "allSamples.bcf"), bcftools_view_options),
])
job.name = "snp_and_indel_bcf.allSamples"
jobs.append(job)
for job in jobs:
job.command = "mkdir -p " + output_directory + " && \\\n" + job.command
return jobs
def rawmpileup(self):
jobs = []
for sample in self.samples:
mpileup_directory = os.path.join("alignment", sample.name, "mpileup")
for sequence in self.sequence_dictionary:
output = os.path.join(mpileup_directory, sample.name + "." + sequence['name'] + ".mpileup.gz")
gzip_job = Job([], [output])
gzip_job.command = "gzip -1 -c > " + output
job = pipe_jobs([
samtools.mpileup([os.path.join("alignment", sample.name, sample.name + ".sorted.dup.recal.bam")], None, config.param('rawmpileup', 'extra_mpileup_options'), sequence['name']),
gzip_job
])
job.command = "mkdir -p " + mpileup_directory + " && \\\n" + job.command
job.name = "rawmpileup." + sample.name + "." + sequence['name']
jobs.append(job)
return jobs
