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That avoids useless transfer and that also avoids creating .1, .2, .3, ... files
when the original file already exists

Now KmerSegmenter.segmented_germline always contains the last tested germline, even
when it is not actually segmented.

core/segment.{h,cpp}: both V and J kmers must be above DETECT_THRESHOLD to flag the germline as 'detected'

This reverts the idea of 41b4f071, but still uses a 'detected' flag.
This flag tells us whether we should continue to the remaining germlines.
In the case of incomplete rearrangements, we certainly want to continue even if we have
many V or many J (but now both of them).
Tests d2a0dbd5 are now passing.

Note that we don't run this test when strand == 2, this should be changed.

The sequence TRDD2-01 is only 9 bp.

MultiGermline::build_incomplete_set() loads incomplete rearrangements into separate indexes.
This is temporary, one day we will parse germline.data, and gather several indexes into one.

See 08182493 and 0ad7c6bd.

-display labels only if necessary
-debug menu
-better scaling

-login page no longer accesible for authentified user (redirect to patient/index)

-parse url arguments and convert them to json
-display_result() : handle data and analysis (so any ajax call who return data or analysis will be accepted)

-big clones are faster (better if they are placed in first)
-collide function will advantage big clones (out of my way!!)
-clone's position can be computed using the n last positions to smooth the animation
-add some magic

Mikaël Salson authored Nov 27, 2014 and Vidjil Team committed Nov 27, 2014

The reason is not clear. But it avoids web2py complaining about not knowing format_size