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This sequence, previously expertised in 84f2acae, fails since cd292aa0.
The tests are now passing.

We run should-vdj-to-tap.py unbuffered (python -u) to have the best tee experience.

The segmentations were previously xxx (because of a known bug on the evalue) and are now IGH
as expected. Since there are more affectations in the index, the xxx has more ambiguous
positions now, which increases its e-value.

Due to 9db2ea1c, there is one more test classified as BUG.
(release-2016.08 does not have the right number of expected fails)

Due to 79c2bebc the number of failed tests increase since we changed two TODOs
in BUG

All files inside refer to curated-vdj, not should-vdj

Commits ad0fe37e and 5815bf0d were very lazy, they are reverted.
It is safer to still check all these tests, allowing some failed tests corresponding
to recent or challenging .should-vdj sequences.

Te results of the tests were carefully compared to the ones before ad0fe37e/5815bf0d.
The difference (6 tests) come from some missing D segments due to 0c3cd0e.

as in algo/Makefile

Contains sequences from other files (redundant)

Those files contain fake sequences.

This merge all .should-vdj.fa files into one file, and test this file.

This test is twice faster than an usual 'make shouldvdj_with_rc': it should
be used to quickly check whether these tests run. However, when something fails,
it does not provide precisely the location of the error.

Now all should-vdj tests are also run on the rev-comped sequences.
This increases the test time, but improves our robustness.

When entering mnaually curated sequences, this is faster than launching
a full 'make shouldlocus_and_vdj' (which further recompiles everything).

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

Since cb9d3fea, shouldvdj errors were not taken into account.
This is fixed.

We should not launch a command directly but use variables instead.
The standard variable for make is $(MAKE). It is therefore more portable
(for instance on freebsd where the make command used should be gmake)

All KmerSegmenter should-vdj tests (-2q) are now also run on revcomp'd files (-r), and
should give exactly the same output than the original test files.

Even if it works, we choose to not run FineSegmenter tests with the same option.
It would test nothing more, as the '-c segment' command first calls the KmerSegmenter to select
the best locus with its strand.

cleancoverage removes coverage-related files
cleantests removes test-related files
cleanall removes everything.