GitLab

Put tests specific to segmentation in testSegment()

Several features added (from CRAC's should-to-tap):
- Can ignore any amount of whitespaces
- Can require to match exactly a pattern (no regex: special characters are protected)

- Drag and drop possible to bring back undisplayed time/point inside

- possibilty to put away a point by drag and drop over label "others"
- TODO a menu to take them back

Side effect: no 'clones.vdj.fa' and 'seq/*' files are produced.
The 'vidjil.data' file is still produced.

This is the main Vidjil output (as a fasta file): representatives of the clones, ready to be processed by other tools.
Until now, this output was on stdout and (partially) in out/seq/*

var t was the current position inside the time_order array
now var t is just the current time and time_order is used only to draw graph

js : change method to compute min_size and precision, the min_size depends of the normalization, so we need to recompute min_size and precision value after each normalization

Vidjil should not be used to segment reads.

It could be nicer with python argparse :)

so we need to call update_normalization if the time_order change or if the clone_size change

-update getSize family function in consequences

- click on a clone star icon to open tagSelector
- input expected value for normalization
- click normalize
- magic happens

- adjust some javascript in consequences

The threshold is a percentage, not a ratio.

('segmented.vdj.fa' may be not be the best filename choice, we should change it.)

'removeChevauchement' and possibly other infos

This is a file specific to each people. No reason for versioning

Because of the value for min_cover_representative that has changed (commit
4ee616a) the value computed in that case is now 4 instead of 5. So the
representative is slightly longer which shifted the positions.

The library is now built in core, where we have the list of dependencies
(dep.mk). Before dep.mk was in algo/ but the files it was refering to were in
core/. Thus the dep.mk file was useless.