Commits · a2bf9992f43ca5e9496c7d081559a7832f4087f4 · khalid / radsex

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 3 commits
- Updated doc · 40746221
  Romain Feron authored Apr 17, 2018
  
  40746221
- Faster BWA make · ab8acb14
  Romain Feron authored Apr 17, 2018
  
  ab8acb14
- 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 3 commits
- Updated sex distribution output · ba4c2f01
  Romain Feron authored Apr 16, 2018
  
  ba4c2f01
- Updated doc with full usage and a quick start guide · 2783c62a
  Romain Feron authored Apr 16, 2018
  
  2783c62a
- Updated command line interface to match doc · 7fa84ee6
  Romain Feron authored Apr 16, 2018
  
  7fa84ee6
13 Apr, 2018 4 commits
- Started updating readme · b8effb59
  Romain Feron authored Apr 13, 2018
  
  b8effb59
- Removed files which are now relevant to radsex-vis · ce9cfadf
  Romain Feron authored Apr 13, 2018
  
  ce9cfadf
- 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 11 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
- cleanup · 4cbeeac0
  Romain Feron authored Apr 03, 2018
  
  4cbeeac0
- Changed license from MIT to GPL3 · 75aa01f6
  Romain Feron authored Apr 03, 2018
  
  75aa01f6
- Removed qtCreator files from master · b2e34ce8
  Romain Feron authored Apr 03, 2018
  
  b2e34ce8
- qtCreator file · a72f0da1
  Romain Feron authored Apr 03, 2018
  
  a72f0da1
- 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
14 Feb, 2018 1 commit
- Setup for filtering function · 96d147c7
  Romain Feron authored Feb 14, 2018
  
  96d147c7
13 Feb, 2018 3 commits
- Added header to group loci output · efbbd962
  Romain Feron authored Feb 13, 2018
  
  efbbd962
- Sex distribution matrix now has 0 at position 0, 0 · e14f2962
  Romain Feron authored Feb 13, 2018
```
Sequences not found in any individual are an artefact of coverage filtering and are not relevant for other analyses
```
  e14f2962
- Removed old code · 6acc386c
  Romain Feron authored Feb 13, 2018
  
  6acc386c
12 Feb, 2018 3 commits
- Fixed min cov output bug · 8fb06b89
  Romain Feron authored Feb 12, 2018
  
  8fb06b89
- Added min coverage to process reads and implemented C-style file write... · 2c9e8b36
  Romain Feron authored Feb 12, 2018
```
Added min coverage to process reads and implemented C-style file write (optimization still necessary)
```
  2c9e8b36
- qtcreator files · cd003639
  Romain Feron authored Feb 12, 2018
  
  cd003639
09 Feb, 2018 1 commit
- Small bugfix in subset max females parameter · 35fc2c60
  Romain Feron authored Feb 09, 2018
  
  35fc2c60
08 Feb, 2018 2 commits
- Fixed output bug for sex distribution · 499b2cfe
  Romain Feron authored Feb 08, 2018
  
  499b2cfe
- Fixed number of males / females bug · b19f1496
  Romain Feron authored Feb 08, 2018
  
  b19f1496