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Mathieu Giraud authored Feb 05, 2015 and Vidjil Team committed Feb 05, 2015

More logical progression: total, segmented, segmented on the selected systems

Mathieu Giraud authored Feb 05, 2015 and Vidjil Team committed Feb 05, 2015

The 'selected' info is now always the number of reads analyzed by the program.

Mathieu Giraud authored Feb 05, 2015 and Vidjil Team committed Feb 05, 2015

m.reads.segmented is updated when one selects some systems by computeReadsSum()
(Perhaps this dynamic value should be called something else...)

This was dead code.

This was dead code, not working, with less features than ./vidjil -u

This was dead code, not working, with less features than tools/align.cpp

As the 'operation' struct now contains the score, the S table is useless.

An homopolymer is now aligned as CC/-C instead of CC/C-.
Side effect from previous commit.

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.

-selected row are keeped between search and config switch

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.

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.