Merge branch 'master' of github.com:MrOlm/pipeCoverage

CHANGELOG.md

@@ -4,171 +4,20 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/)
 and this project (attempts to) adhere to [Semantic Versioning](http://semver.org/).
 
-## [1.2.0] - 2017-19-11
-### fixed
-- Scoring with regards to strain heterogeneity modified
-
-## [1.1.3] - 2017-09-11
-### fixed
-- N50 calculation is now correct
-
-## [1.1.2] - 2017-08-25
-### Changed
-- fixed proper pip sklean-learn (thanks Ben Woodcroft)
-- added the blank folder test_backend/ so that the test suite will work
-
-## [1.1.1] - 2017-07-26
-### Changed
-- added links to ISME publication in readme and documentation
-
-## [1.1.0] - 2017-07-20
-### Added
-- genome input for bonus
-- option to to the 'percent' method for determining taxonomy
-- testing for taxonomy
-- Tdb now includes the columns "best_hit" and "full_tax" (for both methods of determining taxonomy)
-
-## [1.0.0] - 2017-07-14
-### Added
-- bonus --check_dependencies now exists
-- gANI now gives a message when it fails
-
-### Fixed
-- pytest is now automatically installed with pip
-- the logger now does ' '.join(args) when printing the args to run dRep
-- documentation now correctly says "ANIcalculator"
-- makes sure ANIcalculator and checkM work when loading them (even if you can find them in the system path)
-
-## [0.5.7] - 2017-04-26
-### Fixed
-- having the user add their own Chdb now works
-- in bonus, changed an erroneous > to >= when calling centrifuge
-- changed the way the test_suite compares dataframes
-
-## [0.5.6] - 2017-04-23
-### Fixed
-- nc option now works with gANI (controller makes it a float)
-- test_backend is now a thing automatically
-
-## [0.5.5] - 2017-04-09
-### Fixed
-- coverage values at the threshold are now accepted (< instead of <=)
-- setup now automatically installs scikit-bio (needed for MDS plot)
-
-### Changed
-- the loop in which genome lengths are calculated in d_cluster is changed to
-prevent errors when running large numbers of genomes
-
-## [0.5.4] - 2017-03-28
-### Changed
-- default coverage method is now larger (tests are updated to reflect this)
-
-### Fixed
-- gANI now properly computes the coverage using the "larger" method
-- gANI can now tell when it's not installed
-
-## [0.5.3] - 2017-03-28
-### Changed
-- documentation about dependencies changed; versions added as well
-- changed the way ani averaging is done; substantial speed increase when working with very large secondary clusters
-- added the dRep version to the log file
-
-## [0.5.2] - 2017-03-24
-### Fixed
-- prodigal now properly threads for gANI
-
-## [0.5.1] - 2017-03-17
-### Fixed
-- Plot 3 (MDS) now prints onto a square grid
-- Testing suite now launches all tests automatically
-
-## [0.5.0] - 2017-03-16
-### Added
-- The final analyze plot can now be made!
+## [1.0] - 2017-09-21
+### changed
+- Combined pipe_coverage.awk version 0.3 and pcov_tools.py version 0.5 to make combined version 1.0
 
-### Fixed
-- pyenv message
-- log typos
+### added
+- Version file
 
-## [0.4.0] - 2017-03-10
-### Fixed
-- prodigal now multithreads the correct amount
-- compare_wf double-printing issue
-- --SkipMash now works
-
-### Changed
-- default checkM method is now lineage_wf in dereplicate_wf, filter, and choose
-- pyenv now reverences non-anaconda in the documentation and error messages
-- default min length in now 50,000
-
-### Added
-- more thorough testing (though still not nearly enough)
-- log now contains the exact command run
-
-## [0.3.8] - 2017-03-06
-### Fixed
-- Mash sketch size argument actually works now
-
-## [0.3.7]
-### Fixed
-- Fixed analyze to produce non-ugly plots
-
-## [0.3.6]
-### Added
-- Can now change the method of calculating coverage with ANIn
-- Added TODO
-
-## [0.3.5]
-### Fixed
-- Bug that caused the program to crash when looking for Mash
-- Lots of typos (in documentation and program help)
-
-## [0.3.4]
-### Changed
-- Fixed some typos in documentation
-- Added bioRxiv link in documentation
-
-### Fixed
-- Edited matplotlib to make text that can be edited by illustrator
-
-## [0.3.3]
-### Fixed
-- Small bug in telling the user when checkM/prodigal is not in system path
-- Small bug preventing SkipSecondary from working
-
-### Added
-- Test for SkipSecondary
-
-## [0.3.2]
-### Fixed
-- Time estimates now take into account threading
-- Fixed the "choose" operation erroneously taking the "adjust" arguments as well
-- Removed the 'mauve' option as a secondary algorithm
-- Fixed a lot of erroneous logging
-
-### Changed
-- Removed a bunch of commented-out methods
-
-## [0.3.1]
-### Changed
-- READme updated
-
-### Added
-- Documentation
-
-### Fixed
-- A bug where '-h' wasn't working properly
-- Some messages in cluster that should be going to log
-
-## [0.3.0] - 2017-01-30
-### Added
-- Basic functional testing
-- This here Changelog
-- Probably a lot of other stuff that I don't remember (due to the previous lack of Changelog)
+## [0.3] - 2016-11-01
+### fixed
+- Fixed issue in pipe_coverage.awk. When very few reads map, it was still determining the read length based on the RC called in the beginning. Now, I update RC at the end to become j (which will be RC if that value is reached). This effects the start of END
 
-### Changed
-- Moved the argument parsing to a "controller" class
-- The backend of the way the log runs. It's better now
+## [0.2] - 2016-10-15
+### added
+- Added this changelog
 
-## [0.1.0] - 2017-01-15
-- This is the name of the release generated before implementation of a changelog. The development version number for this release was 0.2.3
+### fixed
+- Fixed issue in pipe_coverage.awk. When dealing with buckets, I'm now subtracting 1 from the value before dividing. This is because the value 3000 belongs in bucket 0, not bucket 1. I'm essentially just making ita zero-based value, which is fine because we'll never get a length 0 scaffold or position. This effects lines 11 and 20.