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bamCompare error message typo #966

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alfonsosaera opened this issue Jul 9, 2020 · 1 comment
Closed

bamCompare error message typo #966

alfonsosaera opened this issue Jul 9, 2020 · 1 comment

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@alfonsosaera
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Hi, while running bamCompare as

bamCompare --operation mean --effectiveGenomeSize 2913022398 --normalizeUsing BPM --binSize 50 -b1 sample1.bam -b2 sample2.bam -o sample-MEAN.bpm.bw

I got the error

'--normalizeUsing BPM' is only valid if you also use '--scaleFactorMethod None'! To prevent erroneous output, I will quit now.

so I ran it again adding --scaleFactorMethod None as follows

bamCompare --operation mean --effectiveGenomeSize 2913022398 --normalizeUsing BPM --binSize 50 -b1 sample1.bam -b2 sample2.bam --scaleFactorMethod None -o sample-MEAN.bpm.bw

but got the error

usage: bamCompare -b1 treatment.bam -b2 control.bam -o log2ratio.bw
bamCompare: error: unrecognized arguments: --scaleFactorMethod None

reading the manual of bamCompare I found that the right argument is --scaleFactorsMethod instead of --scaleFactorMethod, note the extra s in the first one.

Thanks for this great package

@LeilyR
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LeilyR commented Jul 9, 2020

Thanks for reporting it. We will fix it.

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