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It was not used.

Some offline usage of the browser could require to properly display a list of files

'config' was used both for conf.js and for the config argument in the URL

The public test server has a new address.
Moreover, there is no need to duplicate this address in main.js.

Configuration files should not be directly versioned.

Mathieu Giraud authored Feb 11, 2015 and Vidjil Team committed Feb 11, 2015

The X axis is now more natural (left to right).
The Y axis could stay in the other direction.

When we are in database mode:
 - these informations were not presented to the user, it is the case now
 - the disclaimer now includes warning on health-related data storage and processing

Mathieu Giraud authored Feb 09, 2015 and Vidjil Team committed Feb 09, 2015

See c0ed6d1e

ReadChooser doesn't use a file.

ReadChooser was storing all the sequences and score in a map (log-time access)
and then reads were stored in a vector which was sorted depending on the
scores stored in the map. So we had many allocations (map+vector) and a slow
access (log access time, so the sort was in n log²n, where n is the number of
sequences). I'm a bit ashamed to have done such an inefficient thing.

Now the scores and the sequences are stored in an array. The sequences
are not copied, but just a pointer to them is stored.

The C function qsort is used because the C++ sort doesn't work
(because of implicit destruction of something).

The code is now much quicker (a -c clones of 600k reads, with -z 1 is now twice as fast).

Someone motivated could probably do better with a radix sort.

For the moment the representative doesn't compute
a quality.

Since we copy the information from the best sequence if the sequence had
quality information, we were also getting it for the representative... and it
was displayed in the .vdj.fa file.

C++11-ready.

Append some flags to CXXFLAGS
and use LDLIBS instead of LDFLAGS for -lm and -lz

See https://www.gnu.org/software/make/manual/html_node/Implicit-Variables.html

Affine gaps are enabled only when using some Costs such as VDJaffine.

Implements affine gaps by storing three matrices, B, Bins and Bdel.

Our github sources are now under the 'vidjil' organization.