Chase Mateusiak

refseq download error

5

I am trying to download a handful of yeast genomes from ref seq with the following script: ``` library(biomartr) library(tidyverse) post_wgd_yeasts = c( "Naumovozyma castellii", "Naumovozyma dairenensis", "Tetrapisispora blattae", "Tetrapisispora...

Add a 'None' option for color

3

First, this is a nice package -- thank you. I would like to highlight some positions in an alignment in a more manual manner. I'm doing this by including some...

[Nextgenmap](https://github.com/Cibiv/NextGenMap) is genomic aligner from [CIBIV](http://www.cibiv.at/). It is useful for identifying SNPs. - [ x] This comment contains a description of changes (with reason). - [ x] If you've fixed...

Picard/ADDORREPLACEREADGROUPS: making args conform to other packages; adding optional index output

5

- modified picard_addorreplacedreadgroups to parse the `ext.args` parameter similarly to how other modules parse it - added an optional emit channel for the index, in the event the flag `CREATE_INDEX`...

[YAHA](https://pubmed.ncbi.nlm.nih.gov/22829624/) is an open-source,flexible, sensitive andaccurate hash-based DNA aligner designed for relatively long queries(approximately 100bp to 32Kbp). [Github repo here](https://github.com/GregoryFaust/yaha). - [ x] This comment contains a description of changes...

There is a suggestion that custom bed formats be specified in the autoSQL format. This seems like a nice tool, but I have only found the docs describing the autoSQL...

gff_recover error

4

I'm getting an error that seems to have to do with my input gff. I have tried with both `gff_remove_feats.rb` and `gff_longest_transcripts.rb` ``` parallel --joblog run/joblog.chainSort -j 15 -a run/joblst.chainSort...

. I am using v0.5.5, and originally submitted with the following cmd: ``` ngm \ -r KN99_genome_fungidb.fasta \ -q run_1272_s_3_withindex_sequence_AAATGCA.fastq.gz \ --threads 2 \ --bam ``` but, I received this...

support passing multiple env files

1

**Is your feature request related to a problem? Please describe.** I would like to be able to pass environmental variables that are stored in separate files, eg: ```bash singularity exec...

In the documentation of [overlap](https://pyranges.readthedocs.io/en/latest/autoapi/pyranges/pyranges_main/index.html#pyranges.pyranges_main.PyRanges.overlap), this is how the `strandedness` argument is defined: > strandedness ({None, "same", "opposite", False}, default None, i.e. auto) – Whether to compare PyRanges on the...