Leandro Hermida

JobLibCollisionWarning: Possible name collisions between functions in same file when only one function exists

3

I occasionally get these specific `JobLibCollisionWarning: Possible name collisions between functions` warning which are not reproducible (if I run the same code again it will only rarely happen, or happen...

NES as a color option in addition pvalue, padjust, qvalue for gseaResult

1

For gseaResult it would be nice to have NES as a color option. Often, users will only plot gene sets that are already signficant, so the NES value is more...

`emapplot` `showCategory` doesn't support providing a vector of names

3

`emapplot` `showCategory` doesn't support providing a vector of names. Most other enrichplot functions and it would be useful.

Number of genes in the core enrichment or gene set alone are not as informative as the gene ratio (# core enriched / # number of genes in gene set)...

Cedar segfaults with SAM files

1

I cannot seem to get Cedar to properly work without segfaulting. My input SAM is produced by PuffAligner against a CAMI example paired-end FASTQ and a Pufferfish index of 100...

PuffAligner significantly slower at mapping and thread usage is much less than specified when running with `--compressedOutput`

1

I've test both with `--compressedOutput` and without, and surprised how much slower `align` is when it is activated, writing of the compressed SAM file becomes a bottleneck to the entire...

Error parsing strand (?) from GFF line

2

It causes the entire program to stop and then I can't use it to perform actions on the file. Here's an example: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/006/247/105/GCA_006247105.1_UU_GM_1.1/GCA_006247105.1_UU_GM_1.1_genomic.gff.gz ``` $ gffread -E GCA_006247105.1_UU_GM_1.1_genomic.gff Command line...

CDS gets filtered out and its attributes overwrite attributes for another CDS in the same gene

2

https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/845/545/GCA_000845545.1_ViralProj14434/GCA_000845545.1_ViralProj14434_genomic.gff.gz When I run with `-F --keep-exon-attrs` to show what happens, these lines: ``` AF234533.1 Genbank gene 1405 2262 . + . ID=gene-P;Name=P;gbkey=Gene;gene=P;gene_biotype=protein_coding AF234533.1 Genbank mRNA 1405 2262 . +...

Segmentation fault or corrupted output GFF when using `-C` coding only option on multiple NCBI genome assembly GFF files

1

https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/843/825/GCA_000843825.1_ViralProj14424/GCA_000843825.1_ViralProj14424_genomic.gff.gz This either segfaults or produces a corrupted output GFF file. I've run into other examples with NCBI genome assembly GFF files.

Normally with gffread I've found that using `--no-pseudo` and `-F` that `--no-pseudo` still filters out all features with a `pseudo=true` attribute. But for this example: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/874/185/GCA_000874185.2_ViralProj20757/GCA_000874185.2_ViralProj20757_genomic.gff.gz This feature with `pseudo=true`...