search

mskilab-org / fragCounter

GC and mappability corrected fragment coverage for paired end whole genome sequencing
MIT License
7 stars 11 forks source link

FragCounter not reading from cov.rds files #8

Open oriolpich opened 3 years ago

oriolpich commented 3 years ago

Hi,

it seems that cov is hardcoded to NULL in PrepareCov within the FragCounter function:

cov = PrepareCov(bam, cov = NULL, ...) in lines 298 and 303.

According to my test, this causes the function to yield an error if a coverage.rds is provided. I managed to run the function by removing the NULL.

cov = PrepareCov(bam, cov = cov, ...)

Hope this helps!