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-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 :)

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

Otherwise the displayed date is ``None'' and when the user validates the form
she has an error message stating that the date is under the wrong format.

HERBERT Ryan authored Sep 22, 2016 and Mathieu Giraud committed Sep 29, 2016

Many tests in this suite were dependant on data from testRunner and
therefore on the order of the execution of each testcase. This commit
encapsulates the test data in order to ensure the order of execution has
no effect on the result of these tests

HERBERT Ryan authored Sep 22, 2016 and Mathieu Giraud committed Sep 29, 2016

Added 'none' options to webserver and init selection so users can opt to
choose their own webserver or startup program

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

run_copy copied the sequence file into the result file. But the filename used was the internal Web2py filename (which is quite long).
And it was reencoded for the results_file which lead to a very long filename which was likely to exceed the limit of the
filename length.
Now we take the original filename for the data file, which will lead to a much shorter encoded filename

Follows a973c9dd

This will help further bug hunting.

A great new feature by @m-salson: Now the generated representative sequences
can span over some ambiguous positions (including some sequencing errors).

Mikaël Salson authored Sep 28, 2016 and Mathieu Giraud committed Sep 28, 2016

--A--T--A--A--C--C--C--T--T--T was matching twice in sequence 2 (shifted by two positions).
The unexpected match covered the position with the difference.

Modifying the example sounds like cheating but the sequence has
very low complexity which makes a not-so-easy test case.

Mikaël Salson authored Sep 28, 2016 and Mathieu Giraud committed Sep 28, 2016

Clang doesn't allow the declaration of a variable-length array
with a non-POD type. Thus we do it the classical way.

Mikaël Salson authored Sep 28, 2016 and Mathieu Giraud committed Sep 28, 2016

For an unknown reason, Clang complained about the line:
seed = IKmerStore<T>::seed
because “error: no viable overloaded '='”
It seemed to interpret one of the variable as const (which is not)
as it indicated:
/usr/bin/../lib/gcc/x86_64-linux-gnu/6.1.1/../../../../include/c++/6.1.1/bits/basic_string.h:565:7: note: candidate function not viable: 'this' argument has type 'const string' (aka 'const basic_string<char>'),
      but method is not marked const

The solution was to use a local variable. Clang was happy, but I don't
see what really makes the difference.

Mikaël Salson authored Sep 27, 2016 and Mathieu Giraud committed Sep 28, 2016

The V gene is not the same following a shorter representative
(see previous commit). This shows that this designation is
not very robus, which is not especially surprising due to the
representative length.

Mikaël Salson authored Sep 27, 2016 and Mathieu Giraud committed Sep 28, 2016

Following modifications in representative computation, and in this case
due to the change in the seed for representative computation, the representative
is one base shorter at the start.