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KChen-lab / Monopogen

SNV calling from single cell sequencing
GNU General Public License v3.0
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file chromosome comparisons #1

Closed grennfp closed 11 months ago

grennfp commented 1 year ago

Thank you for providing this useful tool! I had a quick question about some of the file checks in the Monopogen.py script.

I'm running this with a bam file that doesn't include "chr" in its chromosome names. I initially tried using a reference fasta and vcfs that include "chr" as input to the tool.

I received errors due to chromosome mismatches, prompting me to remove "chr" from the reference fasta and vcfs I was using as input.

These files no longer have "chr" in them, but I still received a chromosome mismatch error. Looking into the code, it looks like on line 81 of Monopogen.py the chromosome is compared with the value 0.

I changed the "0" to "args.chr" as done elsewhere in the script and everything worked fine. Is this check for "0" intended for some reason I missed?

Thank you,

grennfp

jinzhuangdou commented 1 year ago

Do you still face the chr matching issue in the new version?