Breaking Changes

The config yaml file has been restructured to be hierarchical yaml. PLEASE TEST THIS

Full Changelog: 4.0.1...5.0

Minor changes relevant to bioconda installation and running

• LepWrap now has formal installation via /.misc/install.sh
• Working adding it to bioconda
• split out some static file generators as scripts
• little QoL updates
• updated Lep-Map3 and Lep-Anchor modules

remove configfile from rules since it's explicit in the bash wrapper

Several quality of life improvements:

1. Fix #5 by copying the lastz binaries into thhttps://github.com/pdimens/LepWrap/settingse conda environment's bin/ directory only if LepWrap is run inside a conda environment
2. You can now skip LepMap3 or LepAnchor independently
3. LepWrap will notify you if it detects you are not in a conda environment (but does not exit, just let's you know)
4. Second positional argument to LepWrap added, allowing you to specify the config filename, if it's different from config.yml
5. If defaulting to config.yml and if it's not found in the project directory, one will be generated with the same defaults that are in the repo
6. Updated and cleaner logic for edge trimming
7. Edge trimming output now comments out the markers instead of removing them from the file (thanks @kstanx via twitter!)
8. Edge trimming for LepMap3 now rescales the passing markers to 0 (what the LepAnchor trimming was already doing). The removed markers are scaled as well to keep the numerical relationships between markers consistent, in case you wanted to investigate later. (thanks @makopyan)
9. Some optional scripts in scripts/ renamed and comments clarified

Breaking changes

• config.yaml was renamed config.yml

Full Changelog: 3.5...3.6

fixed some silly typos

Changes

• map selection for SeparateChromosomes is more smooth now and cutting it off prematurely wont mess things up
• removed iterations parameter from config.yaml (since the iteration mechanics were changed in a previous release)
  • you can specify iterations in the extra_params instead

New stuff

• params script to pull up the help text for a given LepMap3 or LepAnchor module
  • this is to accommodate use with the extra_params

Changes:

• updated Lep-Map3 binaries to current release (05/05/2021)
• reorganized rules
• split lepanchor rules
• changed folder organization for 10_* (breaking!)
• changed some filenames (breaking!)
• (Lep-Map3) reordering markers uses half as many iterations

New:

• adds third PlaceAndOrientContigs iteration
  • removes discovered haplotypes between iterations 1 & 2
• extra parameters added for Lep* modules for ultimate flexibility

New features

• More plotting improvements
• Messages are more useful

LepAnchor additions

• Adaptive edge trimming and plotting
• Changed folder structure for better organization (breaking!)
• experimental report writing (not activated)