- 11 Oct, 2018 1 commit
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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).
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- 03 Oct, 2018 2 commits
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Mathieu Giraud authored
See also #3502.
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Mathieu Giraud authored
See also #3502.
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- 02 Oct, 2018 10 commits
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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 k-mers close to the first sequence.
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Mikaël Salson authored
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Mikaël Salson authored
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Mikaël Salson authored
A higher p-value threshold will give a lower limit for number of k-mers hence will be more sensitive (but less time-efficient). See #3225
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Mikaël Salson authored
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Mikaël Salson authored
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Mikaël Salson authored
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Mikaël Salson authored
This will ease unit testing
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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 k-mer has matched in the longest possible sequence. Therefore we make the assumption that k-mers matched in the longest sequence but we have no way of knowing as we don't keep track of where the k-mers matched. Fixes #3225
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Mikaël Salson authored
Compute the minimal number of k-mers of an uncertainty range whose mean is given by the empirical number of k-mers found. The probability is provided as an integer as we don't have Z-scores for every possible value and float comparison can be a bit tricky.
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- 24 Sep, 2018 1 commit
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Mathieu Giraud authored
See #3444.
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- 14 Sep, 2018 2 commits
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Mathieu Giraud authored
Factor a code that what called 4 times.
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Mathieu Giraud authored
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- 28 Jul, 2018 6 commits
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Mikaël Salson authored
Fixes #3395
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Cyprien Borée authored
See #3393
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Mikaël Salson authored
See #3393
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Cyprien Borée authored
Will be called when not all the reads can be stored.
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Cyprien Borée authored
See #3393
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Mikaël Salson authored
This will help to reuse those functions elsewhere in the code See #3393
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- 23 Jul, 2018 5 commits
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Mikaël Salson authored
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Mikaël Salson authored
Don't know why and since when (see should#20)
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Mikaël Salson authored
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Mikaël Salson authored
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Mikaël Salson authored
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- 21 Jul, 2018 1 commit
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Mathieu Giraud authored
See #3414.
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- 20 Jul, 2018 10 commits
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Mikaël Salson authored
From #2549
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Mikaël Salson authored
What was tested was not output anymore by fuse.py. This replaces the test with something somewhat similar that is now output. That also ensure the distribution is slightly tested.
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Mikaël Salson authored
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Mikaël Salson authored
The sequence is now correctly found as TRG.
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Mikaël Salson authored
From #2549
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Mikaël Salson authored
The sequence is now correctly found as TRG.
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Mathieu Giraud authored
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Mathieu Giraud authored
See #1409.
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Cyprien Borée authored
For more informations, see #1409.
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Cyprien Borée authored
Now the option can be used with a number in order to export the alternative genes into the json. For more informations, see #1409.
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- 19 Jul, 2018 2 commits
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Cyprien Borée authored
For more informations, see #1409.
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Cyprien Borée authored
This pointer is necessary to have the Bioreader where the N best genes will be exported. For more informations, see #1409.
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