Readcount fix #273
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Readcount fix #273
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necrolyte2
reviewed
Dec 11, 2017
| if cmd_args['config']: | ||
| cmd += ' -c {config}' | ||
| p = run_cmd( cmd.format(**cmd_args), stdout=lfile, stderr=subprocess.STDOUT ) | ||
| tcmd = "samtools view -F 2048 -b {tmp_bam} > {bamfile}" |
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You might want to remove the tmp_bam file to be considerate of space or make that an option
| lofreq = bc_cfg['lofreq']['default'] | ||
| lofreq_options = bc_cfg['lofreq_options']['default'] or '' | ||
| if lofreq: | ||
| cmd1 = 'lofreq call -f {reference} {bamfile} -o {vcf} ' + lofreq_options |
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Did you install lofreq anywhere? I don't see that you added it to conda requirements or other requirements file?
ngs_mapper/runsample.py
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| if cmd_args['config']: | ||
| cmd += ' -c {config}' | ||
| p = run_cmd( cmd.format(**cmd_args), stdout=lfile, stderr=subprocess.STDOUT ) | ||
| r = p.wait() | ||
| if r != 0: | ||
| logger.critical( "{0} did not exit sucessfully".format(cmd.format(**cmd_args)) ) | ||
| rets.append( r ) | ||
| # Variant Calling | ||
| from ngs_mapper.config import load_config | ||
| bc_cfg = load_config(cmd_args['config'])['base_caller'] |
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Only way to use this is to edit config file and use that config file right?
Maybe we can add a flag to run_sample.py as well?
averagehat
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