- 26 Nov, 2014 10 commits
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Mathieu Giraud authored
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Mathieu Giraud authored
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Mathieu Giraud authored
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Mathieu Giraud authored
These options do not exist anymore.
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Mathieu Giraud authored
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- factorize messages in myConsole.msg.database_timeout - set timeouts to at least 5000 (but some others are 15000, this should be defined somewhere in a unique place) - set priority to 1 for non-critical message (access to .data and .analysis)
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When one plays with multi-system files, one often deselects all systems. We do not want to see a 'red' warning in this case.
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- 25 Nov, 2014 15 commits
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Mathieu Giraud authored
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Mathieu Giraud authored
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Mathieu Giraud authored
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Mathieu Giraud authored
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Mathieu Giraud authored
To keep the previous results, one should here select the IGH default seed.
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Mathieu Giraud authored
Additionally, one test has a different output due to a previously forgotten '-d' option.
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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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Mathieu Giraud authored
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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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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 1 commit
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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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