 16 Oct, 2018 12 commits


Mathieu Giraud authored
We require in `vidjilformat.md` the unicity of the `id` fields.

Mathieu Giraud authored

Mathieu Giraud authored
See #3358.

Mathieu Giraud authored
Extracting getClone() to SampleOutput. See #3358.

Mathieu Giraud authored
See #3358.

Mathieu Giraud authored
See #3358.

Mathieu Giraud authored
See #3358.

Mathieu Giraud authored
See #3358.

Mathieu Giraud authored
See #3358.

Mathieu Giraud authored
See #3358.

Mathieu Giraud authored
See #3358.

Mathieu Giraud authored
See #3358. Far from perfect, but allows to gather code.

 11 Oct, 2018 1 commit


Mikaël Salson authored
There is a problem in g++4.8: erase with a const_iterator doesn't exist (while it should: it is c++11).

 03 Oct, 2018 2 commits


Mathieu Giraud authored
See also #3502.

Mathieu Giraud authored
See also #3502.

 02 Oct, 2018 10 commits


Mikaël Salson authored
With #3225 we don't have a fixed limit on the number of sequences to get. We will get all the sequences that have a common number of kmers close to the first sequence.

Mikaël Salson authored

Mikaël Salson authored

Mikaël Salson authored
A higher pvalue threshold will give a lower limit for number of kmers hence will be more sensitive (but less timeefficient). See #3225

Mikaël Salson authored

Mikaël Salson authored

Mikaël Salson authored

Mikaël Salson authored
This will ease unit testing

Mikaël Salson authored
Rather we use an uncertainty range (see #3225 for why and how). It is necessary to get the length of the longest transferred sequence as it will be used as a reference to compute the empirical probablity that a kmer has matched in the longest possible sequence. Therefore we make the assumption that kmers matched in the longest sequence but we have no way of knowing as we don't keep track of where the kmers matched. Fixes #3225

Mikaël Salson authored
Compute the minimal number of kmers of an uncertainty range whose mean is given by the empirical number of kmers found. The probability is provided as an integer as we don't have Zscores for every possible value and float comparison can be a bit tricky.

 24 Sep, 2018 1 commit


Mathieu Giraud authored
See #3444.

 14 Sep, 2018 2 commits


Mathieu Giraud authored
Factor a code that what called 4 times.

Mathieu Giraud authored

 28 Jul, 2018 6 commits


Mikaël Salson authored
Fixes #3395

Cyprien Borée authored
See #3393

Mikaël Salson authored
See #3393

Cyprien Borée authored
Will be called when not all the reads can be stored.

Cyprien Borée authored
See #3393

Mikaël Salson authored
This will help to reuse those functions elsewhere in the code See #3393

 23 Jul, 2018 5 commits


Mikaël Salson authored

Mikaël Salson authored
Don't know why and since when (see should#20)

Mikaël Salson authored

Mikaël Salson authored

Mikaël Salson authored

 21 Jul, 2018 1 commit


Mathieu Giraud authored
See #3414.
