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Ruitulyu / KAS-Analyzer

New computational framework to process and analyze KAS-seq and spKAS-seq data.
MIT License
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normalize function won't run without assembly id, but documentation says assembly id is optional #10

Closed ecroot closed 12 months ago

ecroot commented 1 year ago

Describe the bug The usage message for KAS-Analyzer normalize says

-s [assembly id]: please input the reference genome assembly id of bedGraph files. e.g. Human: hg18, hg19, hg38; Mouse: mm9, mm10, mm39; C.elegans: ce10, ce11; D.melanogaster: dm3, dm6; Rat: rn6, rn7; Zebra fish: danRer10, danRer11. Note: the assembly id need to be consistent with the normalized KAS-seq bedGraph files. REQUIRED only if -b was specified.

However, the command

KAS-Analyzer normalize -m ratios -k KAS-seq_data.txt -r ratios.txt

which does not specify -b, results in the following error:

Error: unsupported assembly id:

To Reproduce Run a simple normalize command without -b and -s

Expected behavior The behaviour of the command and the documentation should match: either the documentation needs to state that the parameter is required, or the tool needs to allow the parameter to be optionally supplied.

Ruitulyu commented 12 months ago

Hi, Thanks! The bug has already been fixed. Best, Ruitu

On Fri, Nov 24, 2023 at 5:27 AM E Croot @.***> wrote:

Describe the bug The usage message for KAS-Analyzer normalize says

-s [assembly id]: please input the reference genome assembly id of bedGraph files. e.g. Human: hg18, hg19, hg38; Mouse: mm9, mm10, mm39; C.elegans: ce10, ce11; D.melanogaster: dm3, dm6; Rat: rn6, rn7; Zebra fish: danRer10, danRer11. Note: the assembly id need to be consistent with the normalized KAS-seq bedGraph files. REQUIRED only if -b was specified.

However, the command

KAS-Analyzer normalize -m ratios -k KAS-seq_data.txt -r ratios.txt

which does not specify -b, results in the following error:

Error: unsupported assembly id:

To Reproduce Run a simple normalize command without -b and -s

Expected behavior The behaviour of the command and the documentation should match: either the documentation needs to state that the parameter is required, or the tool needs to allow the parameter to be optionally supplied.

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ecroot commented 12 months ago

Thank you!