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HERBERT Ryan authored Oct 04, 2016 and Mathieu Giraud committed Oct 05, 2016

Altered some condition statements to improve clarity of code

Sequences sent to external website have now an unique identifier.
The clone index is prepended to the getName() (with a # as a separator).

This ensure that no sequence will share a same FASTA header, which could
cause some softwares to complain. Also, when analysing the results, we will
easily know which result belongs to which clone.

The clone index is put at the start rather than the end because
IMGT/V-QUEST cuts the header when it is too long.

At this point identity is a string, which cannot be NaN.
Therefore we start by converting the value to a float and
then we test whether is it NaN or not.

However the value may not be defined (when there are no indels),
in which case it is empty. In such a case we fallback to the
identity % without indels.

-tagselector appear closer to the user mouse
-tagSelector mousehover doesn't shrink the segmenter

-form generator (select samples/systems)
-form validator
-save/restore state mechanism

auto-resize/center

-fix missing args
-fix fake log function to match the signature of the real log function

HERBERT Ryan authored Aug 08, 2016 and Vidjil Team committed Oct 01, 2016

Fixed a bug in the hotfix where I used a python method of checking the
presence of a string in an array.

Ambiguous terms should be surrounded by parentheses

-2 : unexpected recombinations
-3: compute CDR3

We may want to launch the locus tests only without launching the whole test suite.

Never commit in a hurry!

The previous commit (see 8496cbb0) indicated a suffix for the backup files
(necessary with POSIX sed). Then we were overwriting the tap files with the
bak ones. This was totally stupid as we were overwriting the correct files
with the old ones…

This is now fixed we just delete the backup files as we don't really need them
(we just specify the option to ensure the compatibility between POSIX and GNU
sed).

GNU sed and POSIX sed have slightly different behaviors.  Those behaviors are
incompatible if we don't specify a “backup” suffix with -i. So we specify such
a suffix and then we move all the files so that they overwrite the original
files.
Moreover in this case, the -e option is necessary for FreeBSD's sed.

sed may return an error code if there is no tap file in one of the
subdirectory. I didn't find an option in sed to ignore such errors, so ignore
all errors.

Handle DDJ recombinations on TRD.
This corrects one bug but there are still some sequencesthat are not correctly segmented.
This should be further investigated.

-i option should be put before the filenames in FreeBSD sed.

When git is not available or the current directory is not under a git, an
error message is displayed each time the command is launched.

Using $(shell ...) construct the command will be launched at the affectation
and not each time the variable is used.

diffstat may not exist. We must prevent the build from failing because of that

grep may return a non-zero code when some files are unreadable, this
would fail the test which is not desired.

That was a total mess

Thanks to Valgrind.

When the global test suite is passing, individual failed tests (counted in SHOULD_*_EXPECTED_FAILS)
can be marked as 'TODO' to make continuous integration happy

Mikaël Salson authored Sep 22, 2016 and Mathieu Giraud committed Sep 29, 2016

The Federal government asked them to do so
<https://www.ncbi.nlm.nih.gov/home/develop/https-guidance.shtml>.

Yeah… encryption is good :)