1.3

What's Changed

• convert circlize + plotly to BioCircos by @pdimens in #111
• Mergevariants by @pdimens in #113
• custom filenames for DT csv exports by @pdimens in #115

Full Changelog: 1.2.3...1.3

1.2.3

hotfix

• the snp module had a bug where it was calling makeWindows.py instead of the renamed make_windows.py

1.2.2

hotfix

• reporting for phase workflow filters out phase blocks of size 0

1.2.1

hotfix

• empty lines permissible in stitch parameter file

1.2.0

New

• added harpy deconvolve
• added deduplication and deconvolultion options to harpy qc

Internal

-global scripts have snake_case naming conventions

BREAKING

• adapter trimming is now opt-in for harpy qc rather than opt-out

Full Changelog: 1.1...1.2.0

1.1.1

Merge pull request #101 from pdimens/100-impute-create-separate-conda…

1.1

New

• add HPC subcommand and support by @pdimens in #83
• new input model listing abspaths in config.yaml by @pdimens in #88
• Add aggregate report for bx stats by @pdimens in #92
• new harpy resume module

Breaking

• replace minimap with strobealign by @pdimens in #90

Internal

• move pysam into main env by @pdimens in #93
• finding biallelic contigs is much, MUCH faster. (e.g. from 4min down to 0.5s)

Full Changelog: 1.0...1.1

harpy v1.0

New features

• simulating linked reads via deconstructed LRSIM
• auto containerization via singularity
  • new --conda option to disable this
• improved alignment coverage reporting
• snp modules support specifying genomic regions of interest

Changes

• merged alignment reports
• rm HPC option (temporarily)
• most Plotly plots replaced with Highchart plots
• alignment report circos plot now interactive

internals

• CLI entry point changed to cli
• new harpy containterize command (hidden)
• snakemake rerun trigger is now just mtime to force fewer unnecessary reruns
• general code cleanups via linting

Issues and PRs

• fix adapter flag for qc by @pdimens in #65
• internal API overhaul by @pdimens in #73
• replace snp windowsize with regions by @pdimens in #75
• add simulate linkedreads by @pdimens in #76
• Singularity by @pdimens in #77

Full Changelog: 0.9.0...1.0

harpy v0.9.1

hotfix for the harpy qc module where -a (--ignore-adapters) was working opposite how it should have

Full Changelog: 0.9.0...0.9.1

harpy v0.9.0

New features

• align minimap to use minimap2 as an aligner option #60
• simulate * to simulate snps, indels, inversions, cnv, and translocations onto a provided genome

Bugs fixed

• fix -x parameter for qc #62
• various wording improvements

Full Changelog: 0.8.0...0.9.0