nikostr

I'm interested in running cutN to identify all regions of Ns in my sequence. If I'm understanding the code correctly, regions of Ns are interrupted if the score becomes negative,...

I have run kmdiff and identified overrepresented kmers among two groups. Following this, I created a membership matrix to identify kmers present in all my case samples, and intersected these...

Hi! Thanks for this excellent tool! When aggregating or dumping on a run-dir that's read-only, I get the following error: ``` terminate called after throwing an instance of 'gatb::core::system::Exception' [2024-04-27...

Allow specifying sample IDs instead of numbers for kmdiff diff?

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Thanks for this very nice tool! I'm interested in doing some permutations of my groups, in order to get an impression of what a baseline number significant hits is for...

fix: gffread issue with reading gff files, writing fasta files

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The gffread wrapper raises `ValueError: Unknown annotation format` for gff files. In addition to this, the wrapper assumes that any fasta output contains the spliced exons of each transcript (produced...

It would be good to have some documentation regarding deploying private repos using GitHub personal access tokens. From what I understand it currently works as follows: when attempting to deploy...

In the LiftOn output it seems like output with `status=Liftoff` or `status=LiftOn_chaining_algorithm` produces transcript features while output with `status=miniprot` produces mRNA features. Is there a reason why these are not...

One piece of my output looks as follows: ``` ptg000006l LiftOn gene 86505371 86507566 . - . ID=g31624;source=Liftoff ptg000006l LiftOn transcript 86505371 86507566 . - . ID=g31624.t1;Parent=g31624;mutation=frameshift,stop_codon_gain;protein_identity=0.718;dna_identity=0.652;status=LiftOn_chaining_algorithm ptg000006l LiftOn exon...

feat: add `--no-temp` flag synonymous to `--notemp`

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This PR adds a `--no-temp` flag, synonymous to `--notemp`. This resolves https://github.com/snakemake/snakemake/issues/3618. ### QC * [x] The PR contains a test case for the changes or the changes are already...

**Is your feature request related to a problem? Please describe.** The `--notemp` flag does not conform to the naming of several other flags, including `--all-temp` and `--unneeded-temp-files`. **Describe the solution...