Vlad Savelyev

`sequana_coverage` fails with GRCh37

3

GRCh37 chromosome names are pure integers (1, 2, 3, ... in oppose to chr1, chr2, chr3... in hg19/hg38), and at some point when a coverage or a fasta file is...

Input coverage for `sequana_coverage`

1

Hi, Thanks for your work on Sequana. Really appreciate that you are making parts of the pipeline usable standalone, like `sequana_coverage`. I got a couple of requests regarding it. First,...

Assertion `inputR1.eof()` failed [new]

3

I'm having the same error as in https://github.com/Illumina/DRAGMAP/issues/6: ``` dragen-os: /usr/gitc/DRAGMAP-1.3.0/src/lib/workflow/DualFastq2SamWorkflow.cpp:66: dragenos::align::InsertSizeParameters dragenos::workflow::DualFastq2SamWorkflow::requestInsertSizeInfo(dragenos::align::InsertSizeDistribution&, std::istream&, std::istream&): Assertion `inputR2.eof()' failed. ``` However, this time the lengths of sequences and qualities seem to...

Update conda package

1

Currently the 1.3.0 build is failing: https://github.com/bioconda/bioconda-recipes/pull/34744

Reading from stdin

2

Hi, Wondering if it would be possible to support reading input fastq from stdin? It would facilitate re-alignment from a coordinate-sorted BAM/CRAM with [Bazam](https://github.com/ssadedin/bazam), as well as sharding for distributed...

Annotate based on refGene.*.txt.gz

1

Currently, annotation data has to be initialised in 2 steps: 1. Make `RefSeq_knownGene.*.txt` using UCSC browser, 2. Run `generate_refseq_data.py` that reads `RefSeq_knownGene.*.txt` and generates `all_features.*.bed`. After that, `annotate_bed.py` can use...

Fix `GPTSQLStructStoreIndex.load_from_disk`

3

Defaulting to an empty list for `documents` doesn't work here, because it would later fail the check against `None` on this line: https://github.com/jerryjliu/llama_index/blob/main/gpt_index/indices/base.py#L82-L83, which leads to `Only one of documents...

Unified hover: use `legend.tracegroupgap` in mock legend

1

When using a mock legend in the `unified` hover label, read the user-provided `legend.tracegroupgap` parameter instead of hardcoding `tracegroupgap: 7`. To make the tooltip match the legend.

Allow to place legend at the bottom of the bar plot with `barplot_legend_on_bottom`: ```sh multiqc -fv test_data/data/modules -m star --cl-config "barplot_legend_on_bottom: true" ``` Fixes https://github.com/MultiQC/MultiQC/issues/2390 Unrecommended, as it would look...

A new version of the library, plus add the un-minified version to the repo for easier debugging (it won't be embedded into actual reports).