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Get an approximation of the number of sequences in a fasta file
by interpolating from the size of the first 200 sequences.

Note that input->tellg() was not working (not compatible with igzstream ?)

Useful for testing FineSegmentation (which is time-consuming), but the option
is not used yet.

Contrarily to what the commit could let think, there is not so many modifications.
Basically the idea is to use the existing code and to transform generate_to_file
to a recursive function. So when generating a VDJ recombination we first do the
DJ recombination and then by calling the function recursively we use all the V
with the generated DJ.

This reverts 6815ffb5.
With '-x', we need to have some check, even when there is no e-value check.

Try to detect unexpected recombinations

Loading incomplete germlines in the same index may give some problems,
as the same sequences will be loaded several times with different roles,
leading to AFFECT_AMBIGUOUS affectations. We thus ignore the '-1' setting
for incomplete germlines, and do not consider these germline for MAX12 ('-2').

Now '-i' should work with '-1' and/or '-2', and the previous test passes.

n+1 indexes: the n regular ones, and the common one for MAX12.

No-modification change
 - set_index(index) sets the index
 - update_index(index) may be used on any index (including other indexes than the index set)
 - insert_in_one_index and build_with_one_index take a boolean 'set_indexes'

We want to be able to update any index (for example a global one) with sequences of a germline,
without changing the index of this germline.

Giving two KmerAffects, which one is the more on the left ?

The special germline PSEUDO_GERMLINE_MAX12 uses the usual KmerSegmenter,
but launches computeSegmentation() on the two most frequent KmerAffects of the read.

The 'strand' detection is also more flexible here and purely indicative, as
we could even segment chimera reads.

If you really want a Germline without germlines, please do not try to FineSegment.

Who wants to define Germlines without germlines ?

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

KmerMultiSegmenter: TOO_FEW_ZERO (instead of UNSEG_NOISY) iff the e_value is bad globally not either on left or on right

That avoids to recompute them each time the getLeftRightProbabilityAtLeastOrAbove() function is called.

Fix 34068e0b, thanks to Valgrind

TRDD2*01 is exactly 9 bp long. With SEED_9, we have in perfect Dd2 recombinations *one* matching k-mer.
The Dd2 TRD+ indexes have a load of around 0.05% and 0.16% (due to Dd3 or J), and thus, with the current e-value
computation, there is no chance to get a left e-value much smaller than 1e-3.