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KChen-lab / Monopogen

SNV calling from single cell sequencing
GNU General Public License v3.0
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cmd1 bug in Monopgen.py #81

Closed imev2023 closed 1 month ago

imev2023 commented 1 month ago

Hi,

I noticed a syntax error on line 97 in Monopgen.py. The third "cmd1 = " definition needs to be printed on its own line.

cmd1 = cmd1 + " | " + bcftools + " view " + " | " + bcftools +  ' filter -e \'REF !~ "^[ATGC]$"\'  | '  + bcftools  + " norm -m-both -f " + args.reference          cmd1 = cmd1 + " | grep -v \"<X>\" | grep -v INDEL |" + bgzip +   " -c > " + args.out + "/germline/" +  jobid + ".gl.vcf.gz"

to 

cmd1 = cmd1 + " | " + bcftools + " view " + " | " + bcftools +  ' filter -e \'REF !~ "^[ATGC]$"\'  | '  + bcftools  + " norm -m-both -f " + args.reference          
cmd1 = cmd1 + " | grep -v \"<X>\" | grep -v INDEL |" + bgzip +   " -c > " + args.out + "/germline/" +  jobid + ".gl.vcf.gz"
jinzhuangdou commented 1 month ago

Thanks. The bug has been fixed.