The first one must not be the detailed. The detailed is second and
the full detailed is third.

Mikaël Salson authored Jun 20, 2017 and Mathieu Giraud committed Jul 07, 2017

Use OnlineBioReader rather than a Fasta reader

Mikaël Salson authored Jun 20, 2017 and Mathieu Giraud committed Jul 07, 2017

We now have an abstract class to deal with biological sequence files. This
will allow to more easily manage different file types.

This commit only reorganizes the code so that we will be able to add a BAM
reader easily. Functionnally the code should be equivalent to its previous
version.

Some functions that were not used have been removed.

The operator>> has been removed as it was only used in unit testing. This
operator is not convenient as having the filename may be useful to reopen the
file or to know its extension, to guess the filetype.

See #2016

See #1642.

One-letter variable names are not very convenient to work with.

Completes 06ada6e9.

We use this more friendly wording instead of 'representative' for quite some time.
See for example e0d8420c, 02b4bc6d, a7aaee81, d445eca5.

Cosmetic change.

Fixes #2239.

Closes #2157

This should be correctly handled in the browser but we make sure
that no name will be output if the name is empty.

This is the same behaviour as with -c segment.

grep was changed for sed because when no occurrence is found grep
exits with code 1, which is not the case of sed.

See #2211.

These three values come from the germline/*.g file.
See #2155.

Closes #2179.

This makes the code more regular, and fixes #1006.

See #2153.

New features with -g.
-g is the recommended way, -V/-D/-J/-G are more advanced.

The recommended option is now '-g germline/homo-sapiens.g'.

Defers to core/germline.cpp the possible failure in opening the file.
Completes the previous commit to fix #2134.

The .g files will be now referred as "germline/homo-sapiens.g", instead of
the longer and redundant "germline/homo-sapiens.germline".
This will improve readability at several places, and is
far more meaningful than the previous "germline/germlines.data".

Fixes #1987.

See #1987.

See #1987.

The default index will be set to Aho-Corasick when we'll
consider that it is ready. For now, option -q (quick) can launch AC automaton

Makes it ready to support a parameter to choose the index.

As indexes can be finish()-ed, we must add that possibility for germlines too

The seed must be given to the germline.

Discussed in #2003. The e-value depends on the number of (segmented) representatives,
not the total number of clones.

Follows what is done for D in e6ffb915, and what was already done for V/J in -c segment.
Even if it may be counter-intuitive, the results of segmentation thus actually depends on the number of reads:
'-e 1' should mean that we expect one false positive segmentation in the output.
Even if some e-values slightly change, this commit does not affect the results of the tests.

We should investigate what happens when a FineSegmenter fails here.
Moreover, is it sane to have the same '-e' paramater for fixing both e-values of Kmer and FineSegmenter?
Or should we rather have another paramater?

Mikaël Salson authored Sep 27, 2016 and Mathieu Giraud committed Sep 28, 2016

We may not want to hard-code the contiguous seed (particularly for the tests).
We may also want to provide the spaced seeds, but it is not possible at the
moment. We will see if it appears to be useful.

Interesting sequences *always* have labels.

This reverts bf2f96fe and d317535b.

After more than one year experience with -t 100 we realised that trimming leads to:
– missing special cases where the V gene is heavily trimmed
– giving bad unsegmentation causes: UNSEG only J appeared in cases where it didn't make sense
  those unsegmentation causes were replaced by UNSEG only V when changing -t to 0 (that also let us think that we could miss some V genes)

However -t 0 does have a drawback that should be addressed. It is more likely to have
spurious hits of V genes in the N-region (particularly with VDJ recombinations
where the N-region is longer). Those spurious hits tend to shift the window towards
the J gene.

In the tests the modifications are due either to slight changes in number of windows
(a small increase due to the previous reason) or to an increase in unsegmentation
with really large windows (since windows are shifted we may not have
enough space left to put a window).