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This was not a .fa file, and now it contains all reads.

Now 'out_unsegmented' causes are output in segment.cpp, displaying affectation for each germline

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.

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.

Mathieu Giraud authored Nov 25, 2014 and Mathieu Giraud committed Feb 02, 2015

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)

This should be corrected.

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.

All the germline stats are now updated in core/windowExtractor.cpp.

Mathieu Giraud authored Jan 31, 2015 and Vidjil Team committed Jan 31, 2015

Now the 'info' link on each point gives more information.

Mathieu Giraud authored Jan 31, 2015 and Vidjil Team committed Jan 31, 2015

Same pattern than getSampleTime

This option is sponsored by UPMC.

Such as TRD/TRD+

In each of the germline, mark as ambiguous the k-mers appearing in another germline.

Marks as AFFECT_AMBIGUOUS kmers from another germline