make filtering the GTF and downstream steps optional
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@iraiosub is already working on this.
Since Mar 24, 2025.
enhancement
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Description
Is your feature request related to a problem? Please describe
Add flexibility in dealing with annotations by making the filtering of the GTF file (using transcripts - either user inputted or longest) optional.
Describe the solution you'd like
when --filter_by_transcripts or a similar flag is enabled, filtering is skipped and only segmentation and regions files directly output by icount-mini are used in downstream analyses
Describe alternatives you've considered
Additional context
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