4.0.1

Minor changes relevant to bioconda installation and running

4.0

• 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

link with zenodo

3.6.2

Update README.md

3.6.1

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

3.6

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

3.4

fixed some silly typos

3.3

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

3.2

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

3.1

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)

3.0

This release has SO MANY breaking changes. It's absolutely not backwards compatible in any way whatsoever.

Breaking changes

• re-implementation of ordering iteration within OrderMarkers2 rather than externally
  • no more need for multiple files per ordering iteration
  • no more need to find best likelihoods
• removal of best-finding rules
• summary scripts changed to accommodate change above
• folder naming structure now sequential
• LepMap3 and LepAnchor deps now in software folder
• config.yaml has new params, dropped threads_per
• Snakefile now named LepMap3.smk

New Features

• LepAnchor support now included. Batteries included!
  • Automates repeat-masking and chainfile creation (the worst parts of the process)
• The plots created by the scripts (like Trim/QA plots) are a LOT nicer and more descriptive
• iteration mechanics now make the pipeline even more flexible and there are fewer performance bottlenecks (faster!)

Fixes

• SeparateChromosomes2 summarization wasn't working correctly and replaced by a bulletproof R script