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dariober / SICERpy

Python wrapper around the popular ChIP-Seq peak caller SICER
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Can not pass species to SICER.py #8

Closed ashrosewood closed 6 years ago

ashrosewood commented 6 years ago

I just installed your latest version and noticed that I get the following error when I tried to use SICER.py while providing a species with the option --species as indicated on your readme. 

SICER.py: error: unrecognized arguments: --species hg19

I noticed if you look at the help from the command line, there is no species option available :

SICER.py -h
usage: SICER.py [-h] [--treatment TREATMENT] --control CONTROL
                [--effGenomeSize EFFGENOMESIZE] [--requiredFlag REQUIREDFLAG]
                [--filterFlag FILTERFLAG] [--mapq MAPQ]
                [--redThresh REDTHRESH] [--windowSize WINDOWSIZE]
                [--gapSize GAPSIZE] [--fragSize FRAGSIZE] [--keeptmp]
                [--version]

Could you look into this discrepancy? Thanks, Ashley

dariober commented 6 years ago

Hi- Indeed, the README file was outdated (now fixed). The --species option is no longer needed since chromosome sizes are extracted from the header of the input bam files. Thanks for reporting this!