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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.

In order to refactor the filter file into a class, the useless constants and
include were removed from the file.

For more informations about the refacotr see #3283.

With g++-8 we had a “warning: catching polymorphic type * by value”.
This is solved by using a reference

Touching it updated its last modification date which triggered the recompilation of vidjil.cpp.
We don't touch it anymore. Therefore the file may not exist and the diff may fail. We just ignore
error messages. In such a case the mv will be executed and the file will then exist.

Fixes #3309

Fix testGetMultiResults when there is only unknown K-mer

See merge request !222

Remove compiler warnings

See merge request !221

Since the map only contain one unknown k-mer it is useless to iterate over it
using a loop.
Also the tap_test method has been changed to the tap_test_equal because of the
equality comparison.
For more informations, see #3303.

see #3303 for more informations

The previous test was only looking for a single unknown K-mer in the map even
though the map shouldn't contain anything else from unknown K-mers.
Indeed when there is no K-mers in the automaton that match the input sequence,
then the map contains only unknown K-mers.
For more informations, see #3303.

The relation between _SYMBOL and _CHAR was not clear and could be
ambiguous. This should clarify a little.

See #3250.

Feature a/3250 shift kmer ascii value for ambiguous and unknown

Closes #3250

See merge request !220

For more informations see #3250.

For more informations see #3250.

Since these two K-mers need to be printed with a different char, this char
is defined as a new macro used exclusively to represent the K-mer in a string.

For more informations see #3250.

For more informations see #3250.

Since the methods returns the same thing, the getLabel instructions can simply
return the toStringValues function result.

For more informations see #3250.

the toStringValues for those two K-mers must be '_' and '?' respectively.
Even though their char macro is 1 and 0 (non printable characters).

For more informations see #3250.

To fit issue #3250 the macros values were changed.
Char n°0 for ambiguous and char n°1 for unknown K-mer.

The only are .should-locus tests.

Close #3294.

Close #3287.

We now have a public Gitlab CI status.
See #3287.

Loading HTTP URL from the file menu

See merge request !210

Fix #3015

Use the macro UNUSED for mandatory parameters that are not
used within functions.

See #1233

Remove compiler warnings

See #1233

should@0ac73002

Resolve heuristic bug with overlapping k-mers

Closes #3296

See merge request !215

vidjil.cpp: refactor option handling using CLI11

Closes #2732, #2749, #2741, and #2738

See merge request !105

No process before its preprocess

Closes #3289

See merge request !209

Feature c/1943 correlate clones

See merge request !198

Mathieu Giraud authored Jun 04, 2018 and Mikaël Salson committed Jun 18, 2018

- as 'id' is defined and is not nucleic sequence, it is removed from highliting fields
- sortBySize changed due to change of read numbers

Mathieu Giraud authored Jun 04, 2018 and Mikaël Salson committed Jun 18, 2018

See #1943. Find perhaps a more relevant place.