- 13 Jun, 2018 3 commits
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Cyprien Borée authored
For more informations see #3268
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Cyprien Borée authored
The FineSegmenter constructor handles the filtering of the germline. By default the value is "NO_LIMIT_VALUE", which means the filtering isn't active. For more informations about it #3268.
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Cyprien Borée authored
See #920 and #3190. (squashed from earlier commits)
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- 29 Jan, 2018 1 commit
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Mikaël Salson authored
This can be useful to align against a collection without the bandwidth optimisation (see #2767).
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- 28 Jan, 2018 1 commit
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Mathieu Giraud authored
core/segment.{h,cpp}, core/windowExtractor.cpp, core/windows.cpp: renames, 'isJunctionChanged', SEG_CHANGED_WINDOW
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- 17 Jan, 2018 4 commits
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Mathieu Giraud authored
Completes a76116be.
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Mathieu Giraud authored
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Mathieu Giraud authored
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Mathieu Giraud authored
Windows can be either shortened or shifted.
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- 16 Jan, 2018 4 commits
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Mikaël Salson authored
Warn when we have one. This requires to add a new segmentation status. The problem is that Segment::getSegmentationStatus() returns just an integer which doesn't make possible to have several statuses at once (which could be convenient). A solution would be to use masks for the statuses (ie. if s is the status we would store 1 << s). Since this would require quite some code modification to achieve that, I added some extra tests (that's bad) to deal with the case where the segmentation is achieved with a shorter or shifted window. In such a case we warn the user in the JSON (warning on the CLI should be done too). See #2913, #2916.
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Mikaël Salson authored
It is good to know so that we can warn the user. See #2913
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Mikaël Salson authored
It was hard to make some tests (eg. unsegmentation-causes.should-get) have a too short window. Modifying a constant just so that the test passes is bad practice, but this is not the case here (at least I believe so). Having difficulties to have a too short w also meant that in practice we would almost never see a “too short w” again. This could be nice. But we know that the position of the window is not accurate (it is not designed to be). Therefore 20nt, if they are perfectly centered may be ok. But we know that it may not be well centered (and we even allow some shifts). Therefore 30nt seems to be a safer limit. See #2913
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Mikaël Salson authored
See #2913
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- 07 Jul, 2017 1 commit
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Mikaël Salson authored
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
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- 14 Mar, 2017 3 commits
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Mathieu Giraud authored
See #1580.
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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
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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- 24 Jan, 2017 1 commit
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Mathieu Giraud authored
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- 06 Aug, 2016 1 commit
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Mathieu Giraud authored
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- 05 Aug, 2016 1 commit
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Mathieu Giraud authored
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- 25 Jul, 2016 1 commit
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Mathieu Giraud authored
A @rchikhi set with ~150M reads tested with all locus gave an e-value multiplier >2^31, leading to integer overflow and many spurious clones. Moreover, the previous multiplier was only an 'int', depending on the actual implementation. The multiplier is now a float (double) value.
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- 06 Jul, 2016 1 commit
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Mathieu Giraud authored
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- 23 Apr, 2016 2 commits
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Mathieu Giraud authored
Preliminary implementation, for vdj_assign
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Mathieu Giraud authored
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- 22 Apr, 2016 1 commit
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Mikaël Salson authored
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- 01 Mar, 2016 3 commits
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Mathieu Giraud authored
Clean stdout. We just report here the JUNCTION, including Cys104 and Phe118/Trp118.
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Mathieu Giraud authored
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Mathieu Giraud authored
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- 28 Feb, 2016 3 commits
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Mathieu Giraud authored
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Mathieu Giraud authored
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Mathieu Giraud authored
This was realized after prototyping and tests by @flothoni. As in IMGT/JunctionAnalysis, the detection relies on the positions of Cys104 and Phe118/Trp118. The detection is here in O(n), taking advantage of the already aligned V and J segments. The current implementation will not give a precise positions when there are insertions or deletions between Cys104 and the end of the V segment (or between the start of J segment and Phe118/Trp118). This could be improved by backtracking the DP matrix.
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- 06 Feb, 2016 3 commits
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Mathieu Giraud authored
This further cleans the code and allows to output D1/D2 boxes as well.
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Mathieu Giraud authored
One day, we may change '5del' and '3del' fields, their naming is not so consistent.
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Mathieu Giraud authored
Bug detected thanks to a full Valgrind.
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- 05 Feb, 2016 3 commits
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Mathieu Giraud authored
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Vidjil Team authored
We do not want to detect twice the same D gene. Note that we do not currently forbid alleles of a same gene. Discussion between @flothoni, @mikael-s, and @magiraud.
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Vidjil Team authored
When a D has already been detected, we do not want to detect anything inside this D. Before this commit, spurious D detections could happen in the EXTEND_D_ZONE. Discussion between @flothoni, @mikael-s, and @magiraud.
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- 02 Feb, 2016 3 commits
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Mathieu Giraud authored
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Mathieu Giraud authored
We need to store sequence_or_rc in the Segmenter.
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Mathieu Giraud authored
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