GitLab

For more informations see #3268

Since a new parameter has been added to filterBioReader (representing the
filter specifity) it has to be transmitted when calling the function. Otherwise
the filter will do the filter on "NO_LIMIT_VALUE".

For more informations see #3268

Since a new parameter has been added, even the germline constructor call
in the test need to use it to use the automaton.

For more informations see #3268.

A boolean parameter has been added in the Germline constructors in order to
check if the automaton needs to be constructed or not.
For example with -Z all, the automaton is not constructed.

For more informations see #3268

The FineSegmenter constructor handles the filtering of the germline. By default
the value is "NO_LIMIT_VALUE", which means the filtering isn't active.

For more informations about it #3268.

In #3268 we want to add a specific command-line option for the filtering.
The -Z has only been declared in the getopt. The remaining task is to
check if -Z still has NO_LIMIT_VALUE as an argument. If so the automaton
is not built, otherwise the automaton is built and the argument is used to
filter the BioReader.

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

This constant is representing -Z 0 parameter. It's used when the filter function
is called on every k-mer with at least one match.

For more informations see #3276

Since in the future there might be another automaton (automaton_3), the
pair_automaton variable has been changed to automaton_5 in many files.

see #3267 and #3267 (comment 96152)

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

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

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.

For the purpose of adding the -Z option (described in #3264), the -H option
will show its description.

Incidentally close #3271.

Sequences are equal before 110bp so the alternative is valid.

For more informations see #3262

Since some sequences are identical, we can add them as a result for
the test.

For more informations about it, see #3223 and #3262.

Since some sequences are identical, we can add them as a result for
the test.

For more informations about it, see #3223 and #3262.

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

For more informations about it, see #3223

For more informations see #3217

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

This test assure that when a sequence is used to filter a BioReader, we
find the sequence back in the result when we provide '1' as the most significant
K-mer.
Also it assures that the final BioReader has a size less than the original one.

For more informations see #3217

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

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

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

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

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)

To avoid dealing with the ascii n°94 and n°63 (for the ambiguous and unknown)
the strand changed (so the ascii value is above 127)

For more informations see #3250

The toString method in KmerAffect was not using the already created methods
toStringSigns and toStringValue.

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.

See #3238.

(squashed from earlier commits)

See #920 and #3190.

(squashed from earlier commits)

See #920 and #3191.

(squashed from earlier commits)