Clarify genome size error and update usage documentation
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Description
Description of the bug
When running with --genome GRCh38, I get the following failure.
WARN: =============================================================================
--macs_gsize parameter has not been provided.
It will be auto-calculated by 'khmer unique-kmers.py' using the '--read_length' parameter.
Explicitly provide '--macs_gsize macs3_genome_size' to change this behaviour.Both '--read_length' and '--macs_gsize' not specified! Please specify either to infer MACS3 genome size for peak calling.
The issue is that --macs_gsize is rejected when using --genome. So the user has to specify --read_length instead. The warning message should be updated. The usage documentation should also be updated to include documentation on both parameters.
Command used and terminal output
Relevant files
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System information
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Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by tracing the command-line handling for --genome, --macs_gsize, and --read_length, then locate the warning and usage documentation entry points. Confirm the behavior when --genome GRCh38 is used with --macs_gsize, update the warning and document both parameters in usage output, and verify the resulting messages.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics, cli, documentation
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100