These options do not exist anymore.

Mathieu Giraud authored Nov 26, 2014 and Vidjil Team committed Nov 26, 2014

- factorize messages in myConsole.msg.database_timeout
- set timeouts to at least 5000 (but some others are 15000, this should be defined somewhere in a unique place)
- set priority to 1 for non-critical message (access to .data and .analysis)

Mathieu Giraud authored Nov 26, 2014 and Vidjil Team committed Nov 26, 2014

When one plays with multi-system files, one often deselects all systems.
We do not want to see a 'red' warning in this case.

To keep the previous results, one should here select the IGH default seed.

Additionally, one test has a different output due to a previously forgotten '-d' option.

This option was again source of confusion (running Vidjil without options was anyway non meaningful).
Now a V(D)J segmentation is run when a compatible germline is given (-D, -G, or -g),
and the correct D parameters are selected.

This was source of confusion, in particular in selecting or not D parameters.
Now the code is cleaner.

Use the power of emacs and org-mode to produce HTML files from Org files

Filesize is given in bytes (B) not in octets ;)
And the K, M, G prefixes are international standards for
10^3, 10^6 and 10^9 not 2^10, 2^20 and 2^30 ;)

Thanks to a question from AF (Rennes)

- more friction and more speed
- result > less bounce
- remove old collide function

Mathieu Giraud authored Nov 22, 2014 and Vidjil Team committed Nov 22, 2014

ABIGUOUS_THRESHOLD becomes DETECTED_THRESHOLD, such reads are flag 'detected'

This is cleaner: on one side we have the cause of unsegmentation, on the other we have the
flag 'detected' if there were enough V+J (now total V+J, we don't need to have both V and J).
Currently, the flag can be set when SEG_+/, TOO_FEW_V/J, or DELTA_MIN/MAX (but not STRAND).

We do not continue to the remaining germlines when 'detected' or STRAND.

This fixes a8d2c873. The idea was good, but not the code.

Again, this sequence should not be segmented on IGL, but reported as AMBIGUOUS on TRG and not TOO_FEW_J.

Getting UNSEG_AMBIGUOUS is not a normal situation. When it happens, we want
to exit and to report this sequence to the user, and not to segment by chance
the sequence on another germline.