Commits · master · rki_bioinformatics / PathoLive

19 Sep, 2019 5 commits
- Update LICENSE file README.md · 5dedcc6e
  Simon H. Tausch authored Sep 19, 2019
  
  5dedcc6e
- Update LICENSE · 34fb3976
  Simon H. Tausch authored Sep 19, 2019
  
  34fb3976
- Merge branch 'master' into 'master' · e5b34fc4
  Simon H. Tausch authored Sep 19, 2019
```
Master

See merge request SimonHTausch/PathoLive!3
```
  e5b34fc4
- -H parameter no longer required. · 9489f14d
  Tobias P. Loka authored Sep 19, 2019
  
  9489f14d
- Adapted hemorrhagic organisms in BSL score list to match organisms names in the default database. · d27a49e5
  Tobias P. Loka authored Sep 19, 2019
  
  d27a49e5
22 May, 2019 1 commit
- Update typo in CCHV in belgian_bsl_scores_always_highest.txt · 91e79761
  Simon H. Tausch authored May 22, 2019
  
  91e79761
11 Apr, 2019 1 commit
- add phage names and parser · 0ff143ad
  simonhtausch authored Apr 11, 2019
  
  0ff143ad
14 Mar, 2019 1 commit
- Merge branch 'master' into 'master' · 1d3960db
  Simon H. Tausch authored Mar 14, 2019
```
HiLive2 migration

See merge request SimonHTausch/PathoLive!2
```
  1d3960db
11 Mar, 2019 2 commits
- Added --config parameter to set more detailed HiLive2 parameters. · ab867c39
  Tobias P. Loka authored Mar 11, 2019
  
  ab867c39
- Removed error parameter from HiLive1 version. · 41aab453
  Tobias P. Loka authored Mar 11, 2019
  
  41aab453
13 Feb, 2019 1 commit
- Improved some help messages. · f6cc7a9d
  Tobias P. Loka authored Feb 13, 2019
  
  f6cc7a9d
12 Feb, 2019 2 commits
- Removed unnecessary files in Collapsible_Tree_with_Amounts. · b28eac0a
  Tobias P. Loka authored Feb 12, 2019
  
  b28eac0a
- HiLive2 integration · 9613080f
  Tobias P. Loka authored Feb 12, 2019
  
  9613080f
24 Apr, 2018 1 commit
- Change name to PathoLive globally · 33282d8a
  Herr Simon Tausch authored Apr 24, 2018
  
  33282d8a
17 Dec, 2017 1 commit
- use all available threads for output · 45a18d36
  Simon H. Tausch authored Dec 17, 2017
  
  45a18d36
13 Dec, 2017 1 commit
- correct pseudocounts, was missing at one position · af7b7f29
  Simon H. Tausch authored Dec 13, 2017
  
  af7b7f29
12 Dec, 2017 1 commit
- add pseudocount to weighted score to prevent missing single reads · 24ada22d
  Simon H. Tausch authored Dec 12, 2017
  
  24ada22d
10 Dec, 2017 1 commit
- add HiLive modes to options · f7f29769
  Simon H. Tausch authored Dec 10, 2017
  
  f7f29769
16 Oct, 2017 1 commit
- Add data directory to prelim_data · dfac5790
  Simon H. Tausch authored Oct 16, 2017
  
  dfac5790
29 Aug, 2017 2 commits
- delete uniquereadsfile · 0bebc989
  Simon H. Tausch authored Aug 29, 2017
  
  0bebc989
- bamfile parser skips non-unique reads. · 795c6d5d
  Simon H. Tausch authored Aug 29, 2017
  
  795c6d5d
18 Aug, 2017 2 commits
- alignment score cutoff is now in hilive · c511bcf3
  Simon H. Tausch authored Aug 18, 2017
  
  c511bcf3
- make compatible with multicycle-output from hilive · 1c55f7cc
  Simon H. Tausch authored Aug 18, 2017
  
  1c55f7cc
09 Aug, 2017 4 commits
- initialize first version of README.md · 3e554706
  Simon H. Tausch authored Aug 09, 2017
  
  3e554706
- add background data resource · 7e7e483b
  Simon H. Tausch authored Aug 09, 2017
  
  7e7e483b
- add background data resource, generalize background generation · d0a8ea31
  Simon H. Tausch authored Aug 09, 2017
  
  d0a8ea31
- use pysam for bam- and sam-reading, remove own cigar-interpretation, clean up code · 5614ed1d
  Simon H. Tausch authored Aug 09, 2017
  
  5614ed1d
08 Aug, 2017 2 commits
- switch cutoff to minimum alignment score from maximum edit dist, delete... · 2fae808d
  Simon H. Tausch authored Aug 08, 2017
```
switch cutoff to minimum alignment score from maximum edit dist, delete function join_samfiles, fix filenames
```
  2fae808d
- removed join_samfiles, entered new filenames · babd9ecb
  Simon H. Tausch authored Aug 08, 2017
  
  babd9ecb
07 Jun, 2017 1 commit
- add scripts for background definition · e6cdd310
  Simon H. Tausch authored Jun 07, 2017
  
  e6cdd310
23 May, 2017 1 commit
- Refactor/rename buttons and variables for visualization · 69022d3f
  Simon H. Tausch authored May 23, 2017
  
  69022d3f
21 Nov, 2016 1 commit
- fix tile detection · ad8cb861
  Simon H. Tausch authored Nov 21, 2016
  
  ad8cb861
25 Aug, 2016 1 commit
- Change program path to actual place of the program instead of the working directory · 66726226
  Simon H. Tausch authored Aug 25, 2016
  
  66726226
22 Aug, 2016 1 commit
- Implement new weighted score: · 563ee05c
  Simon H. Tausch authored Aug 22, 2016
```
Ratio of fore- and background covered bases
```
  563ee05c
19 Aug, 2016 4 commits
- Add all files needed for execution · 80c396dc
  Simon H. Tausch authored Aug 19, 2016
  
  80c396dc
- Merge branch 'master' of https://gitlab.com/SimonHTausch/HiLiveViral · 85a94b8e
  Simon H. Tausch authored Aug 19, 2016
  
  85a94b8e
- Introduce new danger level (lowest/grey for phages) · 7abb9dfb
  Simon H. Tausch authored Aug 19, 2016
  
  7abb9dfb
- Ignore uppercase characters in BSL-Dict -> leads to more hits · 60eff9aa
  Simon H. Tausch authored Aug 19, 2016
  
  60eff9aa
12 Aug, 2016 1 commit
- clean branches · e5c48438
  Simon H. Tausch authored Aug 12, 2016 and Simon H. Tausch committed Aug 12, 2016
```
remove empty line
```
  e5c48438
11 Aug, 2016 1 commit
- Add -C (cutoff) parameter, by which hits are ignored. · 6dcbed4a
  Simon H. Tausch authored Aug 11, 2016
  
  6dcbed4a