Joshua C. Randall issues

Results 25 issues of


Joshua C. Randall

lsf-drmaa forces `SUB_NOTIFY_END` when `output_path` is set unless undocumented `prepand_report` configuration option is set

We have spent the past few days tracking down an issue in which LSF-DRMAA wasn't working on our cluster. In our cluster, `bsub -N` and `bsub -B` are disabled, and...

unverified

Update error function to allow multiple arguments

Fixes #517 and other issues in which some invocations of `error()` pass multiple arguments which are then silently ignored.

upstream HEAD commit not printed when upstream_head_commit not found in rev-list

During a subrepo push, when upstream_head_commit is not found in the rev-list, the error message printed does not contain the actual commit ID, leading to confusion as it seems like...

add filename and error message to 'error closing output file' error in samtools sort

fixes #2049

samtools sort incorrectly reports ENOSPC error from fdatasync while writing temporary outputs as "error closing output file"

#### Are you using the latest version of [samtools](https://github.com/samtools/samtools/releases/latest) and [HTSlib](https://github.com/samtools/htslib/releases/latest)? If not, please specify. (run `samtools --version`) ``` samtools 1.20 Using htslib 1.20 Copyright (C) 2024 Genome Research Ltd....