Commits · 2d1d170acd03a0784069e3821c56f56289dee2c8 · khalid / radsex

05 Apr, 2019 1 commit

Added command line with number of markers to the markers table. First... · 2d1d170a

Romain Feron authored Apr 05, 2019

Added command line with number of markers to the markers table. First re-implementation of 'loci'. Added zenodo DOI to readme

2d1d170a

02 Apr, 2019 2 commits
- Implemented parameters to control significance threshold and to disable bonferroni correction · f3ac4bdb
  Romain Feron authored Apr 02, 2019
  
  f3ac4bdb
- Major code cleanup. Rewrote CLI and parameters system entirely using CLI11. · cc72651f
  Romain Feron authored Apr 02, 2019
```
CLI should be frozen until 1.0.0 hopefully. Setup for implementing the last changes before 1.0.0
```
  cc72651f
01 Apr, 2019 1 commit
- added personal tests and valgrind output to gitignore · e86c5826
  Romain Feron authored Apr 01, 2019
  
  e86c5826
28 Mar, 2019 1 commit
- Removed unused code files, cleaned up file and function names, merged some... · 3f53a6e9
  Romain Feron authored Mar 28, 2019
```
Removed unused code files, cleaned up file and function names, merged some files for better organization
```
  3f53a6e9
21 Jan, 2019 2 commits
- Added header for depth output file · 7a8bae01
  Romain Feron authored Jan 21, 2019
  
  7a8bae01
- implemented computing number of reads for each individual in the coverage table · a0272060
  Romain Feron authored Jan 21, 2019
  
  a0272060
29 Oct, 2018 1 commit
- Removed unused demultiplexing code · 0a592601
  RomainFeron authored Oct 29, 2018
  
  0a592601
08 Oct, 2018 1 commit
- Fixed second bug with . in file names in process_reads (this time for the individual name) · 9edaf1b5
  RomainFeron authored Oct 08, 2018
  
  9edaf1b5
04 Oct, 2018 1 commit

Fixed a mistake when implementing solution for files with '.' in their names.... · 2d23a4a2

RomainFeron authored Oct 04, 2018

Fixed a mistake when implementing solution for files with '.' in their names. Added a check so that the program quits when no input file was detected

2d23a4a2

01 Oct, 2018 3 commits
- Fixed problem with detecting extensions when . was in the file name · 541d1901
  Romain Feron authored Oct 01, 2018
  
  541d1901
- Permissions · 73f60d22
  RomainFeron authored Oct 01, 2018
  
  73f60d22
- Permissions · 1edaa226
  RomainFeron authored Oct 01, 2018
  
  1edaa226
13 Sep, 2018 1 commit
- Permissions - junk · 7bbbc0e0
  RomainFeron authored Sep 13, 2018
  
  7bbbc0e0
05 Sep, 2018 1 commit
- Permissions - junk · 8342dd5f
  RomainFeron authored Sep 05, 2018
  
  8342dd5f
23 Jul, 2018 2 commits
- Updated error message for --output-format · dc11e0de
  Romain Feron authored Jul 23, 2018
  
  dc11e0de
- Implemented fasta output for signif and subset · e3b49cdf
  Romain Feron authored Jul 23, 2018
  
  e3b49cdf
10 Jul, 2018 1 commit
- Handle spaces in string type parameter values · 995c5bfc
  Romain Feron authored Jul 10, 2018
  
  995c5bfc
13 Jun, 2018 1 commit
- Make clean for libraries and fixed bug in file extension detection · 9fe76b5b
  Romain Feron authored Jun 13, 2018
  
  9fe76b5b
20 Apr, 2018 1 commit
- Added messages for steps · a2bf9992
  Romain Feron authored Apr 20, 2018
  
  a2bf9992
18 Apr, 2018 1 commit
- Implemented computing scaffold lengths before mapping · 3be93c58
  Romain Feron authored Apr 18, 2018
  
  3be93c58
17 Apr, 2018 1 commit
- Updated sex distribution and mapping output to add signif field · f5609b8e
  Romain Feron authored Apr 17, 2018
```
Moved mapping output to output module for clarity. Still need some doc
```
  f5609b8e
16 Apr, 2018 2 commits
- Updated sex distribution output · ba4c2f01
  Romain Feron authored Apr 16, 2018
  
  ba4c2f01
- Updated command line interface to match doc · 7fa84ee6
  Romain Feron authored Apr 16, 2018
  
  7fa84ee6
13 Apr, 2018 2 commits
- Tentative process_radtags fix for file names with . in them · 6eb8588e
  Romain Feron authored Apr 13, 2018
  
  6eb8588e
- Fixed bug with p-value lower than precision of a double · cbd417de
  Romain Feron authored Apr 13, 2018
```
Added a minimum value of 10^-16 for p-values
```
  cbd417de
10 Apr, 2018 1 commit
- Minor fixes to mapping and stats · 9ee178c8
  Romain Feron authored Apr 10, 2018
  
  9ee178c8
06 Apr, 2018 2 commits
- Implemented mapping function · 555d0a7f
  Romain Feron authored Apr 06, 2018
  
  555d0a7f
- Setup for mapping function using BWA · 0267d6aa
  Romain Feron authored Apr 06, 2018
  
  0267d6aa
05 Apr, 2018 1 commit
- Created files for mapping module · d519ddde
  Romain Feron authored Apr 05, 2018
  
  d519ddde
03 Apr, 2018 7 commits
- Finished implementing new output + added parameter to output in old format · 75df6777
  Romain Feron authored Apr 03, 2018
  
  75df6777
- Formatting · d19ba5b9
  Romain Feron authored Apr 03, 2018
  
  d19ba5b9
- small bug fixes for new sex distribution output · c889dcb2
  Romain Feron authored Apr 03, 2018
  
  c889dcb2
- Implemented new output for sex distribution table · 0c43f907
  Romain Feron authored Apr 03, 2018
  
  0c43f907
- Added typedef for sex distribution results · b3c016e8
  Romain Feron authored Apr 03, 2018
  
  b3c016e8
- Refactored chi squared calculation into a separate file · 949a1144
  Romain Feron authored Apr 03, 2018
  
  949a1144
- Minor help text change · 9ff064bf
  Romain Feron authored Apr 03, 2018
  
  9ff064bf
07 Mar, 2018 2 commits
- removed debug output · 588fdb8d
  Romain Feron authored Mar 07, 2018
  
  588fdb8d
- Implemented extraction of sequences significantly associated with sex - debugging on genotoul · 78ed159e
  Romain Feron authored Mar 07, 2018
  
  78ed159e
05 Mar, 2018 1 commit
- Added min_individuals and max_individuals parameters to subset · f4b39ca8
  Romain Feron authored Mar 05, 2018
  
  f4b39ca8