See #3307 and next commit.

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.

Replays 42e01d24. Thanks to @mikael-s.

Works with g++ 4.9.
See #2935.

Replays 86e788fc.

Some options will be not always displayed in the help message.
Replays da89488c.

Replays d971892b.
See #2739.

The cache was not freed creating memory leaks.
This code comes from samtools (as all the code
from unbam)

Prepares next commit.

Some options will be not always displayed in the help message.

See #2739.

From https://github.com/CLIUtils/CLI11

See #926.

See #926

Revert 717eea9e. Actually this produced more warnings for all gcc versions
than we had for some versions of clang.

See !72.

The features we use seem to be working with g++ 4.8.

See #2615

Now compiles with g++ 7 (and also with older versions)

See #2615

unbam is a C library, we thus have to include the *.c files

Library to read bam files extracte from htslib

"$(CXX) -M > dep.mk" also needs a "-std=c++11" flag

This should be more portable than --std=gnu++11.

from https://github.com/docopt/docopt.cpp
We need first to evaluate this on simple programs before deciding to use in vidjil.cpp.

We want to be able to test coverage on different rules, without
deleting previous coverage files.

Append some flags to CXXFLAGS
and use LDLIBS instead of LDFLAGS for -lm and -lz

See https://www.gnu.org/software/make/manual/html_node/Implicit-Variables.html

istream initializes the buffer buf while gzstreambase constructor opens the file and
may set some flags (in case the file can't be opened). If istream is called last
it will overwrite the flags that have been set