Mark Diekhans

A FLAIR user had a confusing invalid UTF8 decode error with the process of a SAM file from minimap2. It turned out that the FASTQ used as input was actually...

Addd PDF plot output option

1

It would be really useful if driver scripts passed through a --pdf option to generate publication-quality plots;

python error querying biosample id

3

``` pip install git+https://github.com/pachterlab/ffq % ffq --version ffq 0.3.1 % ffq SAMN20207153 [2025-10-13 22:32:26,336] INFO Parsing sample SAMN20207153 [2025-10-13 22:32:26,338] ERROR 'NoneType' object has no attribute 'text' usage: ffq [-h]...

The following error occurs when I try to install from the 'package-list-packages' buffer: ˘˘ ``` Install package ‘groovy-mode-20230318.533’? (y or n) y forward-sexp-default-function: Scan error: "Containing expression ends prematurely", 2235,...

RM produces an alignment with negative query coordinates

1

**Describe the issue** RM produced an alignment with a negative query coordinate (see below). This is not detected and causes rmToTrackHub to crash (#375) **Reproduction steps** Run by Hiram's UCSC...

**Describe the issue** rmToTrackHub.pl exits 0 (success) even if bedToBigBed. falis After discovering a corrupt bigbed align file, went back to look in the logs and found this: ``` Unsigned...