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A very long time ago, 'out/segmented.vdj.fa' was considered to be
the main output of Vidjil, giving the (heuristic) segmentation of
each read. However, when many reads are segmented, writing this file
to the disk can slow the software (until 25%)... and this file
was used only to debug. By default, this file is now not produced.

The main output, with a summary of windows and representative, is in
'out/windows.fa', 'out/seq/clone.fa-' and now 'out/vidjil.data'.

We will soon produce segmented.vdj.fa only when it is requested.

This should ease debug when receiving mails from Jenkins.

2014/06/17 Marc's email plus a few updates.

We have already a private Jenkins server running the tests. We now test travis-ci.org.

Fails since 49046ca6, no more 'others' are reported

waiting for a better check in checkBrowser()

Mathieu Giraud authored Sep 05, 2014 and Vidjil Team committed Sep 05, 2014

--merge was confusing, this option is meant to merge several .data files with multiple germlines
(note that it works only with one sample)

Mathieu Giraud authored Sep 05, 2014 and Vidjil Team committed Sep 05, 2014

Corrects bug introduced by 92519fc9

Mathieu Giraud authored Sep 05, 2014 and Vidjil Team committed Sep 05, 2014

Additionaly, reports in .data 'germline_V' and 'germline_J'

TODO : auto-compute others clones with javascript

suggestion by Nikos
Now the format 2014.09 is complete, we have to update all parts of Vidjil to deal with the new format.