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 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