- 25 Nov, 2014 6 commits
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Mathieu Giraud authored
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Mathieu Giraud authored
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Mikaël Salson authored
Use the power of emacs and org-mode to produce HTML files from Org files
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Mikaël Salson authored
Filesize is given in bytes (B) not in octets ;) And the K, M, G prefixes are international standards for 10^3, 10^6 and 10^9 not 2^10, 2^20 and 2^30 ;)
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Mikaël Salson authored
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Mathieu Giraud authored
Thanks to a question from AF (Rennes)
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- 24 Nov, 2014 10 commits
- 22 Nov, 2014 4 commits
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Mathieu Giraud authored
ABIGUOUS_THRESHOLD becomes DETECTED_THRESHOLD, such reads are flag 'detected' This is cleaner: on one side we have the cause of unsegmentation, on the other we have the flag 'detected' if there were enough V+J (now total V+J, we don't need to have both V and J). Currently, the flag can be set when SEG_+/, TOO_FEW_V/J, or DELTA_MIN/MAX (but not STRAND). We do not continue to the remaining germlines when 'detected' or STRAND.
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Mathieu Giraud authored
This fixes a8d2c873. The idea was good, but not the code.
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Mathieu Giraud authored
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Mathieu Giraud authored
Again, this sequence should not be segmented on IGL, but reported as AMBIGUOUS on TRG and not TOO_FEW_J.
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- 21 Nov, 2014 11 commits
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Mathieu Giraud authored
Getting UNSEG_AMBIGUOUS is not a normal situation. When it happens, we want to exit and to report this sequence to the user, and not to segment by chance the sequence on another germline.
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Mathieu Giraud authored
When a sequence has both enough V and J affectations (above AMBIGUOUS_THRESHOLD), it should normally be segmented. If not, the sequence is probably a chimera, or the V and J repertoires are not well choosen. We now label this sequence as AMBIGUOUS (instead of TOO_FEW_V or TOO_FEW_J).
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Mathieu Giraud authored
This sequence should not be segmented on IGL, but reported as AMBIGUOUS on TRG.
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Marc Duez authored
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Marc Duez authored
this file was removed by mistake in the last commit
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Marc Duez authored
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Marc Duez authored
-sequence file can be reuploaded -fix missing files -add size
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Marc Duez authored
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Marc Duez authored
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Marc Duez authored
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Marc Duez authored
-renamed in buildBrowsergermline.py
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- 19 Nov, 2014 8 commits
- 18 Nov, 2014 1 commit
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Marc Duez authored
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