- 26 Nov, 2014 1 commit
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Mathieu Giraud authored
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- 25 Nov, 2014 3 commits
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Mathieu Giraud authored
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Mathieu Giraud authored
This option was again source of confusion (running Vidjil without options was anyway non meaningful). Now a V(D)J segmentation is run when a compatible germline is given (-D, -G, or -g), and the correct D parameters are selected.
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Mathieu Giraud authored
This was source of confusion, in particular in selecting or not D parameters. Now the code is cleaner.
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- 07 Nov, 2014 8 commits
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Mathieu Giraud authored
See 183ad875.
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Mathieu Giraud authored
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Mathieu Giraud authored
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Mathieu Giraud authored
This code was duplicated in 60a8bf4a.
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Mathieu Giraud authored
Simplification of the code.
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Mathieu Giraud authored
Closes bug tested by 14b16e9c.
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Mathieu Giraud authored
If -w is below the seed weight (hence the junction size), strange things may happen, as for example a clone without representative.
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- 06 Nov, 2014 2 commits
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Mikaël Salson authored
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Marc Duez authored
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- 04 Nov, 2014 4 commits
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Mathieu Giraud authored
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Mathieu Giraud authored
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Mathieu Giraud authored
(Now only the last option of each is really stored and indexed, see 1a05fe6a.)
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Marc Duez authored
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- 03 Nov, 2014 2 commits
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Mathieu Giraud authored
The CMD_SEGMENT scenario now tries the germlines in the multigermline (until the read is segmented).
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Mathieu Giraud authored
On the default file, Vidjil now returns some clones even with default options.
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- 01 Nov, 2014 1 commit
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Mathieu Giraud authored
As KmerAffectAnalyser is only used with KmerAffect, we do not need to keep the templates. The code should be easier to read for C++ newbies such as the author of this commit.
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- 28 Oct, 2014 1 commit
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Mathieu Giraud authored
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- 24 Oct, 2014 7 commits
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Mathieu Giraud authored
Accessing this method while the window is not label does not create an element in the map.
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Mathieu Giraud authored
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Mathieu Giraud authored
Moreover, now this is exported in .vidjil.
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Mathieu Giraud authored
The usage said it was '-f', but the option was actually '-t'. This option is for now not covered by the tests.
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Mathieu Giraud authored
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Mathieu Giraud authored
Reformulation of 6ec0f991, with a short notice on usage
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- 22 Oct, 2014 6 commits
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Mathieu Giraud authored
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Mathieu Giraud authored
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Mikaël Salson authored
* .data files are renamed to .vidjil * by default output filenames have the same basename as the input file Documentation and tests have been updated accordingly
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Marc Duez authored
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Mathieu Giraud authored
This was hardcoded twice in the code.
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Mathieu Giraud authored
This feature was not documented and not used. The browser offers better normalization features.
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- 21 Oct, 2014 1 commit
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Mathieu Giraud authored
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- 20 Oct, 2014 4 commits
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Mathieu Giraud authored
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Mathieu Giraud authored
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Mikaël Salson authored
Fixed thanks to Valgrind.
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Mathieu Giraud authored
This may help the upcoming modularization of vidjil.cpp (Soissons)
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