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

As the germlines are displayed, we should look for '->' to ensure we are on the right line

The -s/-k/-m/-M command line settings are not used with -g or -i.

delta_max values for TRG put in 5384348e were too high.
It allowed IGH sequences to be segmented. The problem won't exist anymore
when taking into accound forbidden k-mers.

We met the case in one patient in Lille (#123). We need to increase delta_max
in such a case.