Since the unit-tests were using the pair instead of a Filter object, a getter
has been created for the pair.

For more informations, see #3283.

Since the pair attribute is stored in the Filter class, there is no need
to put a pair object in the Filter methods. The methods were changed to use
the object attribute, instead of the parameter.

For more informations see #3283.

For more informations see #3283.

This constructor will directly call the buildACAutomaton method. Then
this method will construct the pair<Vector, Automaton> stored in the
FilterWithACAutomaton class.

For more informations see #3283.

The methods filter and buildAutomaton were moved in the newly created
class FilterWithACAutomaton. The signature in filter.cpp were changed
accordingly.

For more informations see #3283.

Remove compiler warnings

See #1233

Cyprien Borée authored Jun 14, 2018 and Mikaël Salson committed Jun 15, 2018

For more informations see issue #3279

Cyprien Borée authored Jun 14, 2018 and Mikaël Salson committed Jun 15, 2018

Since the last way to compare produced segfault (due to undefined behaviour
of the advance method), to bypass this problem we just look at the previous
of occurences to see if it's the same as the last -1.
For more informations see #3279.

Cyprien Borée authored Jun 12, 2018 and Mikaël Salson committed Jun 13, 2018

Since kmer_threshold parameter became a signed int, there's the possibility
that this parameter is a negative number. If it's the case the entire original
BioReader is returned.

Cyprien Borée authored Jun 12, 2018 and Mikaël Salson committed Jun 13, 2018

If the program is call with -Z 0, the filter function use every K-mer with
at least one match. 0 is defined by the constand ALL_KMERS_VALUE in tools.h
For more informations see #3276

Cyprien Borée authored Jun 12, 2018 and Mikaël Salson committed Jun 13, 2018

Since the kmer_threshold parameter became a signed integer, some comparison
were producing sign warnings due to -Wsign-compare g++ compiler.

For more informations see #3270

Cyprien Borée authored Jun 12, 2018 and Mikaël Salson committed Jun 13, 2018

Since the threshold parameter can be -1 the threshold parameter has been switched
to a signed integer (the default int in C/C++).
Also the use of NO_LIMIT_VALUE is used insted of -1.

For more informations see #3270

Cyprien Borée authored Jun 12, 2018 and Mikaël Salson committed Jun 13, 2018

Since the new option -Z will be added, the case where all K-mers will be selected
to filter will be represented by -Z -1.
For more informations about it, see #3268 and #3264.

Cyprien Borée authored Jun 05, 2018 and Mikaël Salson committed Jun 13, 2018

When there is no sequences found in the filtered BioReader it throws a
segfault.

For more informations about it, see #3223

Cyprien Borée authored Jun 05, 2018 and Mikaël Salson committed Jun 13, 2018

To get the genes with the same number of occurences (described in #3217 )

Cyprien Borée authored Jun 04, 2018 and Mikaël Salson committed Jun 13, 2018

The gene counter was already at 1 when doing the first loop since the
previousKmerOccurs was initiated with '0'. To avoid that, it's now initiate
with the value of the first member of the set.

Also a simple simplification for the gene counter (deleted the empty if and
replaced it with the opposite condition)

For more informations #see 3217

Cyprien Borée authored Jun 04, 2018 and Mikaël Salson committed Jun 13, 2018

The comparator checks if the two KmerAffect have the same number of
occurences.
If it is the case, then the Comparator use the comparison operators defined
in the KmerAffect class to compare the KmerAffects.
If the two KmerAffect doesn't have the same number of occurences, the Comparator
returns true for the one that have the most of them.

For more informations see #3217

Cyprien Borée authored Jun 01, 2018 and Mikaël Salson committed Jun 13, 2018

If two K-mers occurs both the same amount of times, we want them both. Even if
the number of significant K-mers is reached.

For example if we want the 10 most significant K-mers but the 4th has two K-mers
with the same value we take them both instead of one.

For more informations, see #3217

Cyprien Borée authored Jun 01, 2018 and Mikaël Salson committed Jun 13, 2018

The ascii shifting is no longer a requirement since the ascii value of a AMBIGUOUS
and UNKNOWN Kmer are above 127 and thus, unreachable.

For more informations see #3250

Cyprien Borée authored Jun 01, 2018 and Mikaël Salson committed Jun 13, 2018

In buildAutomaton the seed parameter wasn't used since it was only provided
through the insert method. It has been fixed.

For more informations see #3217 and #3217 (comment 93122)

Cyprien Borée authored May 31, 2018 and Mikaël Salson committed Jun 13, 2018

Before, when the filtered bioreader contained less than 2 sequences the
original bioreader was returned, it's no longer the case.

See #3239 to know why.

Cyprien Borée authored Jun 12, 2018 and Mikaël Salson committed Jun 13, 2018

See #920 and #3080.

(squashed from earlier commits)