Changelog

1.1.0 (2024-04-26)

Features

add hp (2f35806)
bwa -> bwa-mem2 (c06521e)
clean popoolation functions (bc34d29)
clean preprocess (954e417)
clean up reads (4fe9e6d)
clean up report (9acfcc0)
cleaning up (b65999d)
cleanup (17bcf28)
compute coverage from pileups (126895f)
disable all protected (662c6cc)
extract helpers (840651c)
extract popoolation1 and popoolation2. not tested (6056753)
extract preprocess (f76e4d0)
extract reads (9107ceb)
extract reference. Use custom reference name (eea30c3)
handle dots in the chromosomes (8498cad)
in popoolation2, write population names rather than numbers (ee0b0a3)
leave only coreutils (e493f48)
lint popoolation1 and 2 (d6910a0)
lint R code (b2adead)
multiple window and step sizes in popoolation1 (9be9332)
multiple window and step sizes in popoolation2 (953a880)
parse units, capture stdout to log (49a3f35)
plot coverage (d5e6327)
put hp in its place (453cd09)
put popoolation in its place. add reports (6228cfe)
refactor (968dd57)
refactor get_files (ab7d366)
remove extras (98957ea)
remove gzip dependency. use bgzip instead. use default level (8ca05a7)
remove numpy dependency. update envs (dd9ce40)
remove version from popoolation (93a7edd)
reorder population and chromosome file structure (868be53)
restyle popoolation (7154aea)
separate the mpileup column joining into a script (c967226)
simplify (7998886)
snakefmt (fa0058a)
split rmdup and filter. update envs (22e0803)
update envs (4396634)
use default samtools compression. remove unnecessary sort (2a7ada5)

Bug Fixes

don't ask in target rules for nontarget files (e5bd3fb)
don't keep uncompressed outputs (48320b9)
folder name (8ede5cd)
handle dots in the references (540fb97)
manage properly bwamem2 indexes (6f585f0)
merge conflict (0dfc78d)
run gha on main, master and devel, just in case (4c74cb9)
show badge in readme, disable all-temp in CI (5b035cd)
simpler sample job (aaf249b)
sort populations and libraries to avoid pop2_vs_pop1 (480fb46)
trimmomatic (f047d0c)