- 03 Feb, 2015 4 commits
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Mathieu Giraud authored
This was not a .fa file, and now it contains all reads.
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Mathieu Giraud authored
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Mathieu Giraud authored
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Mathieu Giraud authored
Now 'out_unsegmented' causes are output in segment.cpp, displaying affectation for each germline
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- 02 Feb, 2015 10 commits
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Mathieu Giraud authored
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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.
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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.
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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)
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Mathieu Giraud authored
This should be corrected.
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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.
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Mathieu Giraud authored
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Mathieu Giraud authored
All the germline stats are now updated in core/windowExtractor.cpp.
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Mathieu Giraud authored
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Mathieu Giraud authored
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- 01 Feb, 2015 2 commits
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Mathieu Giraud authored
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Mathieu Giraud authored
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- 31 Jan, 2015 14 commits
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Mathieu Giraud authored
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Mathieu Giraud authored
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Mathieu Giraud authored
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Mathieu Giraud authored
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Mathieu Giraud authored
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Mathieu Giraud authored
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Mathieu Giraud authored
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Now the 'info' link on each point gives more information.
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Same pattern than getSampleTime
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- 30 Jan, 2015 9 commits
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Mathieu Giraud authored
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Mathieu Giraud authored
This option is sponsored by UPMC.
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Mathieu Giraud authored
Such as TRD/TRD+
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Mathieu Giraud authored
In each of the germline, mark as ambiguous the k-mers appearing in another germline.
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Mathieu Giraud authored
Marks as AFFECT_AMBIGUOUS kmers from another germline
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Mathieu Giraud authored
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Mathieu Giraud authored
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- 29 Jan, 2015 1 commit
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Marc Duez authored
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