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