GitLab

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

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.

When a sequence has both enough V and J affectations (above AMBIGUOUS_THRESHOLD),
it should normally be segmented. If not, the sequence is probably a chimera,
or the V and J repertoires are not well choosen. We now label this sequence
as AMBIGUOUS (instead of TOO_FEW_V or TOO_FEW_J).

This sequence should not be segmented on IGL, but reported as AMBIGUOUS on TRG.

this file was removed by mistake in the last commit

-sequence file can be reuploaded
-fix missing files
-add size

-renamed in buildBrowsergermline.py