Codespell wrapper script and filters for HTSlib et al

codespell

#!/bin/sh

skip=`(cat /dev/null $(find . -name 'wt-*' -prune -o -name .gitignore -print) | sed '/^$/d;s&^.*/&&'; printf '.DS_Store,*.dSYM
*.sam,*.bam,*.cram
*.fq,*.vcf
*.bed,*.bai,*.csi,*.crai,*.gz,*.gz.*
*.out,*.expected
aclocal.m4
.git,interesting,wt-*')|tr '\n' ,`

datadir=$HOME/htslib/interesting
exec codespell --ignore-words $datadir/codespell.ignore --exclude-file=$datadir/codespell.exclude --skip "$skip" "$@"

codespell.exclude

.TE

codespell.ignore

alloced
als
fpr
hist
iff
seeked
som
strat

wt-* is my local convention for additional Git working trees. I create extra ephemeral working trees within my main checked out repository directory for a project and have /wt-* in a global excludesfile. git worktree is fantastic.

(And interesting is for notes, data files, etc.)