Commits · 8ce297b2d591ef7faa1542506361be05dbc0edcb · vidjil / vidjil

31 Oct, 2018 1 commit
- core/check-compiler.h: update links to doc · 8ce297b2
  Mathieu Giraud authored Oct 31, 2018
  
  8ce297b2
29 Oct, 2018 2 commits
- tests: update tests · 4243edae
  Mathieu Giraud authored Oct 29, 2018
  
  4243edae
- core/output.cpp: remove duplicate field · b6c52a49
  Mathieu Giraud authored Oct 29, 2018
```
Following a discussion with J. V. Heiden.
```
  b6c52a49
26 Oct, 2018 1 commit
- vidjil.cpp, doc/vidjil-algo.md: pride, VidjilNet · b118541a
  Mathieu Giraud authored Oct 26, 2018
  
  b118541a
24 Oct, 2018 2 commits
- tests: add tests · 6711acc0
  Mathieu Giraud authored Oct 24, 2018
  
  6711acc0
- core/output.cpp: `duplicate_count` · 5fd950ab
  Mathieu Giraud authored Oct 24, 2018
```
See #3590.
```
  5fd950ab
19 Oct, 2018 15 commits
- tests: add tests · 3af3afbf
  Mathieu Giraud authored Oct 19, 2018
  
  3af3afbf
- core/output.cpp: AIRR, "warnings" · 0b8584df
  Mathieu Giraud authored Oct 19, 2018
  
  0b8584df
- core/output.{h,cpp}: getWarnings() · 2673d761
  Mathieu Giraud authored Oct 19, 2018
  
  2673d761
- core/output.cpp: get(), do not create fields when they do not exists · ee4d4625
  Mathieu Giraud authored Oct 19, 2018
  
  ee4d4625
- tests: add tests · ff16f107
  Mathieu Giraud authored Oct 17, 2018
```
Close #3572 and #3573.
```
  ff16f107
- core/output.cpp: more AIRR fields · 81af152d
  Mathieu Giraud authored Oct 17, 2018
```
See #3572 and #3573.
```
  81af152d
- tests: update · 8e36164d
  Mathieu Giraud authored Oct 17, 2018
  
  8e36164d
- tests: testing AIRR output on S22 and X5 · 1e497e54
  Mathieu Giraud authored Oct 16, 2018
  
  1e497e54
- core/output.cpp: getout(), returns a non-escaped string · 13f901e5
  Mathieu Giraud authored Oct 16, 2018
  
  13f901e5
- vidjil.cpp: use SampleOutputAIRR(), output .tsv AIRR · 9426c9a9
  Mathieu Giraud authored Oct 16, 2018
```
See #2828.
```
  9426c9a9
- core/output.{h,cpp}: define and use CloneOutput.reads() · 83e65abd
  Mathieu Giraud authored Oct 16, 2018
  
  83e65abd
- core/output.{h,cpp}: CloneOutputAIRR, SampleOutputAIRR · 657a89ce
  Mathieu Giraud authored Oct 17, 2018
```
See #2828 and #3457.
```
  657a89ce
- core/output.{h,cpp}: Output.get() · e0c43986
  Mathieu Giraud authored Oct 17, 2018
```
See #3358
```
  e0c43986
- tests: add test · 021fc442
  Mathieu Giraud authored Oct 17, 2018
```
Closes #3575.
```
  021fc442
- core/segment.cpp: warn when there are equally probable assignations · 6b4fabc2
  Mathieu Giraud authored Oct 17, 2018
```
See #3575.
```
  6b4fabc2
18 Oct, 2018 6 commits
- tests: update tests · 932b88af
  Mathieu Giraud authored Oct 18, 2018
  
  932b88af
- vidjil.cpp: always use .toOutput(), even with non segmented sequences · 2ea82b2b
  Mathieu Giraud authored Oct 18, 2018
```
Following a discussion with @mikael-s.
We want to have meaningfull names when the sequence is not segmented.
See !320 (comment 126622)
```
  2ea82b2b
- core/segment.cpp: set clone name in FineSegmenter.toOutput() · de88a137
  Mathieu Giraud authored Oct 18, 2018
  
  de88a137
- vidjil.cpp: -c segment, format unique id · 2f78933e
  Mathieu Giraud authored Oct 18, 2018
  
  2f78933e
- tests: add tests · a34cd291
  Mathieu Giraud authored Oct 18, 2018
  
  a34cd291
- core/tools.{h,cpp}: string_of_int(..., pad_to_width) · 18797367
  Mathieu Giraud authored Oct 18, 2018
  
  18797367
16 Oct, 2018 13 commits
- vidjil.cpp: clean, SampleOutput · 2ce9d1d7
  Mathieu Giraud authored Oct 16, 2018
  
  2ce9d1d7
- core/output.cpp: SampleOutput destructor · a3d0ba6a
  Mathieu Giraud authored Oct 16, 2018
  
  a3d0ba6a
- core/output.{h,cpp}: SampleOutputVidjil, out(), with some polymorphism · efe5f363
  Mathieu Giraud authored Oct 14, 2018
```
See #3358.
```
  efe5f363
- tests: update · 38931d16
  Mathieu Giraud authored Oct 14, 2018
  
  38931d16
- vidjil.cpp: -c segment, unique id per sequence · 6bd291b0
  Mathieu Giraud authored Oct 14, 2018
```
We require in `vidjil-format.md` the unicity of the `id` fields.
```
  6bd291b0
- core/tools.h, core/output.h, core/windows.h: move 'junction' definition to tools.h · a3b3a7bc
  Mathieu Giraud authored Oct 13, 2018
  
  a3b3a7bc
- vidjil.cpp: remove json_data_segment and use windowsStorage->sortedWindowsToOutput() · 29d11583
  Mathieu Giraud authored Oct 14, 2018
```
See #3358.
```
  29d11583
- core/windows.{h,cpp], core/output.{h,cpp}: CloneOutput* SampleOutput::getClone(junction junction) · d856b56f
  Mathieu Giraud authored Oct 14, 2018
```
Extracting getClone() to SampleOutput.

See #3358.
```
  d856b56f
- core/vidjil.cpp: use SampleOutput · 3f118111
  Mathieu Giraud authored Oct 14, 2018
```
See #3358.
```
  3f118111
- core/output.{h,cpp}: SampleOutput · 16d32d5f
  Mathieu Giraud authored Oct 13, 2018
```
See #3358.
```
  16d32d5f
- core/segment.{h,cpp}: pass by pointers · 70c2c165
  Mathieu Giraud authored Oct 12, 2018
```
See #3358.
```
  70c2c165
- tests: update · 3002c764
  Mathieu Giraud authored Oct 12, 2018
```
See #3358.
```
  3002c764
- core/segment.{h,cpp}, vidjil.cpp: use setSeg(), define and use Segmenter.toOutput() · 54b205b9
  Mathieu Giraud authored Oct 13, 2018
```
See #3358.
```
  54b205b9