Commits · master · Blaise LI / libhts

11 Feb, 2021 2 commits
- BamFile changed methods name. · 1e705417
  Blaise Li authored Feb 11, 2021
  
  1e705417
- Add option to filter according to strand. · 711099aa
  Blaise Li authored Feb 11, 2021
  
  711099aa
09 Feb, 2021 1 commit
- Keep all bed by default in extract_annot_start.py · 5caa8ef3
  Blaise Li authored Feb 09, 2021
  
  5caa8ef3
05 Jan, 2021 1 commit
- Script to extract reads from bam from bed regions. · 2f357ca8
  Blaise Li authored Jan 05, 2021
  
  2f357ca8
17 Dec, 2020 1 commit
- Gene-list filtering in extract_annot_start.py. · 56cfa04d
  Blaise Li authored Dec 17, 2020
```
Also have setup.py install the script.
```
  56cfa04d
15 Dec, 2020 1 commit
- Added script extracting first positions from bed. · c6820e38
  Blaise Li authored Dec 15, 2020
  
  c6820e38
10 Dec, 2020 2 commits
- No egg here. · 09d8dd85
  Blaise Li authored Dec 10, 2020
  
  09d8dd85
- Trying to avoid pseudo-conflicts with new pip. · a7dbdd88
  Blaise Li authored Dec 10, 2020
  
  a7dbdd88
09 Dec, 2020 2 commits
- Revert to using unofficial pybedtools. · 86b49bd8
  Blaise Li authored Dec 09, 2020
  
  86b49bd8
- Simpler dependencies. · b0f9dc00
  Blaise Li authored Dec 09, 2020
  
  b0f9dc00
24 Sep, 2020 2 commits
- Wrong variable name. · 9d8662b0
  Blaise Li authored Sep 24, 2020
  
  9d8662b0
- Catch stats numeric error. · a763c9a0
  Blaise Li authored Sep 24, 2020
  
  a763c9a0
08 Sep, 2020 1 commit
- Prepare adaptation to newer cluster. · b13207c0
  Blaise Li authored Sep 08, 2020
  
  b13207c0
31 Aug, 2020 1 commit
- Mention copypaste_bigwig_regions.py in README. · 36c90633
  Blaise Li authored Aug 31, 2020
  
  36c90633
27 Jul, 2020 1 commit
- Avoid deprecation warning. · 3e835227
  Blaise Li authored Jul 27, 2020
```
Changed .ix to .loc
```
  3e835227
08 Jul, 2020 1 commit
- Update test for empty DataFrame. · b13393e1
  Blaise Li authored Jul 08, 2020
  
  b13393e1
02 Jul, 2020 1 commit
- Change dependency to scipy. · 1c0ae101
  Blaise Li authored Jul 02, 2020
```
Now needs 1.4.2 or above.
```
  1c0ae101
29 Apr, 2020 6 commits
- Constrain scipy version. · 79c3d0aa
  Blaise Li authored Apr 29, 2020
```
Later will have to enable 1.4.2.
```
  79c3d0aa
- Nicer message. · 39d96816
  Blaise Li authored Apr 29, 2020
  
  39d96816
- Fixing message. · 28de1679
  Blaise Li authored Apr 29, 2020
  
  28de1679
- Adding progression messages. · 2e675cd6
  Blaise Li authored Apr 29, 2020
  
  2e675cd6
- Specify default "mode" argument for numpy.pad. · b5d98f70
  Blaise Li authored Apr 29, 2020
```
It has no default value for older numpy version.
```
  b5d98f70
- Add script to copy and paste bigwig regions. · 7c79f77a
  Blaise Li authored Apr 29, 2020
  
  7c79f77a
24 Mar, 2020 2 commits
- Linting. · cde7fc33
  Blaise Li authored Mar 24, 2020
  
  cde7fc33
- Make slurm-compatible script. · 66415b36
  Blaise Li authored Mar 24, 2020
  
  66415b36
12 Mar, 2020 2 commits
- Further fixing test of existence. · b5c33ec8
  Blaise Li authored Mar 12, 2020
  
  b5c33ec8
- Fix tests in bash. · 89ca9ae9
  Blaise Li authored Mar 12, 2020
  
  89ca9ae9
24 Feb, 2020 6 commits
- Update used token. · 75c46489
  Blaise Li authored Feb 24, 2020
  
  75c46489
- Coherent licence info. · 4441fea3
  Blaise Li authored Feb 24, 2020
  
  4441fea3
- Mention bam2bigwig.sh and citation in README. · 7f9e31de
  Blaise Li authored Feb 24, 2020
  
  7f9e31de
- Fix auto-module-load for Python 3. · 7e9e2ed2
  Blaise Li authored Feb 24, 2020
  
  7e9e2ed2
- Merge branch 'master' of gitlab.pasteur.fr:bli/libhts · 0fdf3851
  Blaise Li authored Feb 24, 2020
  
  0fdf3851
- Add licence. · b8ad92ec
  Blaise Li authored Feb 24, 2020
  
  b8ad92ec
06 Feb, 2020 1 commit
- Auto load modules in bam2bigwig.sh · 4eb4b3b8
  Blaise Li authored Feb 06, 2020
  
  4eb4b3b8
27 Jan, 2020 3 commits
- Using pep518-aware pybedtools. · c4715fde
  Blaise Li authored Jan 27, 2020
  
  c4715fde
- Using auto-cythonizing pybedtools. · fbbe4ad3
  Blaise Li authored Jan 27, 2020
  
  fbbe4ad3
- Back to custom pybedtools. · 6666fe7b
  Blaise Li authored Jan 27, 2020
  
  6666fe7b
22 Jan, 2020 3 commits
- Revert "Back to custom pybedtools." · 3bf44740
  Blaise Li authored Jan 22, 2020
```
This reverts commit 2b8a5ee6.
```
  3bf44740
- Trying normal pybedtools just for libhts. · acafaa97
  Blaise Li authored Jan 22, 2020
  
  acafaa97
- Back to custom pybedtools. · 2b8a5ee6
  Blaise Li authored Jan 22, 2020
  
  2b8a5ee6