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mskilab-org / fragCounter

GC and mappability corrected fragment coverage for paired end whole genome sequencing
MIT License
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fragCounter: error from readChar(): line 924 in fragCounter.R #10

Closed chris-kreitzer closed 3 years ago

chris-kreitzer commented 3 years ago

Hi all,

Installed FragCounter on my local machine, with all the dependencies. I tried running your example provided ./frag -b inst/extdata/chr21.bam -d inst/extdata/gcMAP21/ -w 200, however FragCounter is throwing a warning

In readChar(check_gz, 4): text connection used with readChar(), results may be incorrect (and subsequent issues, etc.)

I found that this message may constitute from line 924 fragCounter.R, and now I am wondering whether my installation went wrong, or my samtools is working incorrect or any other related issue;

Many many thanks for your help!

Best, chris.

mskilab commented 3 years ago

I think this was benign - it's just code to recognize bam vs cram .. in any case have fixed this warning