- 15 Mar, 2017 4 commits
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Mathieu Giraud authored
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Mathieu Giraud authored
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Mathieu Giraud authored
Thanks to landscape.io
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Mathieu Giraud authored
Thanks to @mikael-s. Closes #2253.
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- 14 Mar, 2017 22 commits
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Mikaël Salson authored
Why can't we keep complicated stuff when there exists really easy solutions? The purpose is to test consistency of the segmentation with 1, 6 and 11 reads. Instead of generating the data on the fly we can store the most abundant datasets and use the magic -x option (see 7b314b61) to restrict the dataset to fewer sequences. This will solve some compatibility issues as this test could have some troubles working on some architectures.
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Mathieu Giraud authored
See #1580.
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Mathieu Giraud authored
See #1580.
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Mikaël Salson authored
As the D is short (with one error), we provide the three possibilities. Follows d89f52d8
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Mikaël Salson authored
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Mikaël Salson authored
See #2249
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Mathieu Giraud authored
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Mathieu Giraud authored
Follows 81ac715d.
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Mathieu Giraud authored
Follows 81ac715d.
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Mathieu Giraud authored
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Mathieu Giraud authored
Following f78c6fc3, name these constants in a positive way, as we report these unsegmentation cases.
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Mathieu Giraud authored
With the previous changes, one may have e-value computations on short sequences, leading to a possibly negative number of k-mers in getProbabilityAtLeastOrAbove(). Fixes #2107.
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Mathieu Giraud authored
We set a meaningful e-value. Moreover, after closer inspection, we find that one sequence may be a genuine 'only V'. See #2107.
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Mathieu Giraud authored
Now that we check e-values to get UNSEG_ONLY_V/J status, an e-value of 1.0 is not meaningful here. See #2107.
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Mathieu Giraud authored
There were previously two places where the segmentation could fail with UNSEG_ONLY_V/J. The first one, when there is no 'good' segmentation point, was improved by 5298c86f, requiring at least 5 k-mers. It turned out that it was not sufficient, as reported by @flothoni in #2107. Contrarily to what what thought in 5298c86f, the segmentation point returned by kaa->getMaximum() is actually meaningful to compute some e-values, even when kaa->getMaximum().max_found is false. We thus now remove completely some ancient code where the thresholds were based on the number of k-mers, and rely solely on checkLeftRightEvaluesThreshold() to discriminate between these unsegmentation causes. Streamlines the code, and will fix #2107.
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Thonier Florian authored
Opens #2107.
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Mathieu Giraud authored
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Mathieu Giraud authored
Vidjil is now as efficient as a 'sort | uniq -c'. Fixes #1642.
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Mathieu Giraud authored
See #1642.
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Mathieu Giraud authored
See #1642.
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Mathieu Giraud authored
See #1642.
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Mathieu Giraud authored
One-letter variable names are not very convenient to work with.
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- 13 Mar, 2017 14 commits
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Mikaël Salson authored
We could have a leak of some bytes
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Mikaël Salson authored
Prevent valgrind to be launched on this test (ie. valgrind on valgrind)
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Mikaël Salson authored
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Mathieu Giraud authored
Completes 06ada6e9.
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Mathieu Giraud authored
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Mathieu Giraud authored
We use this more friendly wording instead of 'representative' for quite some time. See for example e0d8420c, 02b4bc6d, a7aaee81, d445eca5.
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Mathieu Giraud authored
Cosmetic change.
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Mathieu Giraud authored
Fixes #2239.
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Mathieu Giraud authored
Confirms #2239.
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Mikaël Salson authored
Useful when viewed through web interfaces (e.g. on Gitlab/Github). Otherwise comments could be ignored.
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Mikaël Salson authored
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Mikaël Salson authored
Some architectures fail on that test because of errors in libstdc++ on some architectures. We ignore those errors.
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Mikaël Salson authored
Follows 5d910513 and related to #1824
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Mathieu Giraud authored
Following cbcff399 ?
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