v1.1.0

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)