GitLab

This method is used to transfer sequences from a BioReader to another based on
a KmerAffect.

For more informations see #3282.

isGeneric is a method returning true if the current K-mer is not odd (ambiguous, unknown).
It is used instead of calling successively isAmbiguous() || isUnknown()...

SPECIFIC_KMERS_NUMBER is a constant representing the amount of odd K-mers. For now there is
only two (ambiguous/unknown) but in the future it might grow.

For more informations about it, see #3282.

Coverage reports

Closes #1696

See merge request !227

They are thus more easily accessible through Gitlab interface

Depending on the activation of Gitlab Pages (and on my
own understanding of this feature…)

This is better than specifying it in the project settings.

As pointed out by @magiraud the files may not be present
anymore on the slave to analyse the coverage. We therefore
need to pass them as artifacts.

Tests are now launched with coverage included.
A specific job will recover the coverage

lcov needs to know the whole path to a file in order to display it
and to count the coverage on each file.

However when launching with Gitlab-CI, each job is launched in a separate directory
which leads to different paths for the same source files.
Therefore we first remove the trailing path when generating the
lcov files. But we add it again before generating the HTML output
as it requires to access the files.

This prevents from re-using old data.

It allows to add several tests done independently which is convenient
with several independent jobs as we have under Gitlab CI.

Exclude tools from coverage computation

We also remove coveralls as we don't use it anymore

When testing we want to check asserts

This variable is non-standard. We should prefer using CXXFLAGS instead.
This eases passing the --coverage option to sub-makes while avoiding
code duplication (for managing CXXFLAGS and OPTIM)

However overriding CXXFLAGS is not a good idea as it keeps expanding the
variable.

Those flags need to be exported.

Replays 42e01d24. Thanks to @mikael-s.

Feature a/2935 update json

See merge request !223

Works with g++ 4.9.
See #2935.

May help #3315.

Déplacer les déclarations d’options à côté des invocations app.add_option / add_flag

See merge request !212

See #2732 and !212.

feature-a/3283 refactor filter.cpp to class Filter, report informations on filtering

See merge request !214

For more informations see #3283.

Since the filter operates only on the bioreader n°5, its name has been changed.

For more informations, see #3283.

For more informations see #3283.

For more informations see #3283.

For more informations see #3283.

For more informations see #3283.

For more informations, see #3283.

For more informations, see #3283.

For more informations, see #3283.

Since the pair is now contained in the FilterWithACAutomaton class, it is no
so consistent to encapsulate a pair instead of two objects.

For more informations see #3283.

A useless pair was still in a test in testFilter.
Also the pointer for the Filter object is deleted in the end.

For more informations, see #3283

The destructor wasn't checking if the pair was null and so for its members.
It's no longer the case.

For more informations see #3283.

Since Filter class now deal its own memory, there's no need to manually do
it in the testFilter file.

For more informations, see #3283.

Since the Germline now contains a Filter object instead of an automaton
and respectively Filter contains the automaton. Both of them have to
free the memory allocated correctly.

For more informations, see #3283.

Since the function testBehaviourWhenHugeBioReader in testFilter was
using pair and not Filter object, it now use the filter object getter for
the pair.

For more informations, see #3283.

Since the function testExAequoKmersWhenSignificantParameter in testFilter was
using pair and not Filter object, it now use the filter object getter for
the pair.

For more informations, see #3283.