Tests: Delete index in test to avoid Valgrind complaints
Tests: Remove \s+ regexp, unnecessary

Whitespaces are ignore by default. No need for the complicated \s+ regexp.
Additionnally that doesn't work under FreeBSD
Bikeshading: White color by default.

After hours of debate the group decided, at the unanimity of present people, that we should use
the light theme by default.
Compare-all: Positions start at 0 (until nb_clones-1)

We should only consider positions < nb_clones, not <=.
core/tools.cpp: spaced_int(), directly computes an int index from an int* sequence
core/kmerstore.h: new ArrayKmerStore.getResult() implementation, using directly spaced_int

The previous IKmerStore.getResult() (still used in MapKmerStore) had several string malloc/free through spaced(), accounting for a good part of the total time of the heuristic.
This implementation should be faster.

Thanks Mikaël for the solution of the C++ template nightmare :)
core/kmerstore.h: .getResults, B=0 if not ACGT, not 4
testAffectAnaluser.cpp: test also MapKmerStore
tests/testAffectAnalyser.cpp: debug values
core/kmerstore.h: ArrayKmerStore.getResult() 'else' case, no (revcomp_indexed && no_revcomp)

Curiously, omitting this case make fail only some unit tests, but no should_get tests.
What does this 'else' case mean ? Is it really used in Vidjil ?
Tools: Function for converting a nucleotide to an integer.

Use bitwise operations which avoids branching with if/switch.
Tests added
Tools: Use nuc_to_int instead of switch/case
Tools: dna_to_int

Was done in IKMerStore but we should provide it as a tool. Now IKmerStore uses the function dna_to_int.
Tests added.
Tools: revcomp_int performs revcomp on an integer.

Revcomp directly on an integer.
Tests added
KmerStore: With int-value kmers we must also deal with revcomp (if needed)
Tools: inlining spaced_int and nuc_to_int
Tools: Simplification of nuc_to_int

Relying on a wrong binary conversion of A, C, G, T doesn't help in devising
an instruction for converting nucleotides to integers…
Tests: Number of windows change from 9811 to 9809

N is now transformed to T (because of bitwise operations) instead of A and it appears
that a window already exists with a T, so the number of distinct windows slightly decreases.
Merge branch 'getResults': getResults() improved in KmerStore.

Running time of -c windows is halved.
vidjil: update CHANGELOG after 'getResults' merge