- 05 Feb, 2015 6 commits
-
-
-
-
-
More logical progression: total, segmented, segmented on the selected systems
-
The 'selected' info is now always the number of reads analyzed by the program.
-
m.reads.segmented is updated when one selects some systems by computeReadsSum() (Perhaps this dynamic value should be called something else...)
-
- 04 Feb, 2015 3 commits
-
-
Mathieu Giraud authored
This was dead code.
-
Mathieu Giraud authored
This was dead code, not working, with less features than ./vidjil -u
-
Mathieu Giraud authored
This was dead code, not working, with less features than tools/align.cpp
-
- 03 Feb, 2015 16 commits
-
-
Mathieu Giraud authored
-
Mathieu Giraud authored
As the 'operation' struct now contains the score, the S table is useless.
-
Mathieu Giraud authored
An homopolymer is now aligned as CC/-C instead of CC/C-. Side effect from previous commit.
-
Mathieu Giraud authored
Edit operations, with their score computation and their backtracking information, are now defined in a unique location. The code should thus be more flexible and easier to read and maintain.
-
Marc Duez authored
-
-
Marc Duez authored
-selected row are keeped between search and config switch
-
Marc Duez authored
-
Marc Duez authored
-
Marc Duez authored
-
Mathieu Giraud authored
-
Mathieu Giraud authored
When using different indexes, this is only a cosmetic change. But it prepares ourselves to use an unique index, possibly with a better indexing structure.
-
Mathieu Giraud authored
This was not a .fa file, and now it contains all reads.
-
Mathieu Giraud authored
-
Mathieu Giraud authored
-
Mathieu Giraud authored
Now 'out_unsegmented' causes are output in segment.cpp, displaying affectation for each germline
-
- 02 Feb, 2015 11 commits
-
-
Mathieu Giraud authored
-
Mathieu Giraud authored
Unit tests are passing again. The code is now clearer, as these tests actually tested segmentation on only one germline. We should now have real unit tests on KmerMultiSegmenter.
-
Mathieu Giraud authored
Same tests than multi-{complete,short}.should_get, but this time with -i. Testing for incomplete rearrangements should not prevent the 7 reads from being recognized in the right (complete) system.
-
multi-complete.fa -> 7 reads (1 per system), exact concatenation V+(D)+J, no deletion, no insertion multi-short.fa -> the same 7 reads, but shortened (especially at V end)
-
Mathieu Giraud authored
This should be corrected.
-
Mathieu Giraud authored
This is an important change in how the heuristics works with multi-germlines. Now the segmentation may run 2x to 3x slower (with -g -i), but we ensure that the best germline is selected for each read. This improves the results, in particular with mixed data from regular and incomplete rearrangements.
-
Mathieu Giraud authored
-
Mathieu Giraud authored
All the germline stats are now updated in core/windowExtractor.cpp.
-
Mathieu Giraud authored
-
Marc Duez authored
-
Mathieu Giraud authored
-
- 01 Feb, 2015 2 commits
-
-
Mathieu Giraud authored
-
Mathieu Giraud authored
-
- 31 Jan, 2015 2 commits
-
-
Mathieu Giraud authored
-
Mathieu Giraud authored
-