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Closes #2635.

See #2635.

See #2635.

See #2635, but also #3027.

See #2635.

Closes #3012 and opens #3026.

The {} initializer was buggy on some g++-4.8 versions.

Closes #3023

See #2247 and #3010.

See #3012.

The previous solution was not correct as the variable was
expanded when it was used in the Makefile. Therefore all
the processes were (over)writing their results in the same
file.

Fixes #3018.

Verbosity brings noise rather than signal

-e → -r
\s → [[:space:]]

Make sure that the output directory does exist or create it.

Makefile, algo/Makefile: simplify 'make release' through 'git archive'

Closes #2255 and #2720

See merge request !97

Because of files such as ../INSTALL.org a algo
directory will be created (it appears that
mkdir -p algo/.. does create a algo directory).
Therefore we need to remove it.

Fix valgrind issues

See merge request !146

When the add() method raises an exception the reader was not deleted.
This is now corrected. Fixes 3d8ff242

bam_entry was not properly deleted.
We need to call bam_destroy1 so that it is correcly deleted.

Fixes a3175eb0

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

By default Valgrind should be launched in a “classical” way.
The --error-exitcode=1 is added so that the Gitlab job can
fail with Valgrind errors.

To have the XML output, one should add XML_OUTPUT=1 on the command
line when invoking make.

See #3015.

The fa_read could be uninitialised causing a warning.

Fixes #3013

See #3003.