- 16 Mar, 2015 2 commits
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This adds a 'format' optional argument to db.call('admin/log').
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We should use regexps here.
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- 14 Mar, 2015 5 commits
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Some <tr> rows shall not have cursor:pointer.
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The default call to XML() should be safe enough to prevent XSS attacks.
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It may be useful to inspect some data referred in a log.
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- 13 Mar, 2015 11 commits
- 12 Mar, 2015 14 commits
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Mikaël Salson authored
Thanks to Paulo Alexandre Borges Miranda http://stackoverflow.com/a/19595496/1192742
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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
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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
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Mikaël Salson authored
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Mikaël Salson authored
Makefile: Allow to launch a single functional test with valgrind by prefixing its name with valgrind_
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Mikaël Salson authored
This has no consequence since this rule is forced anyway.
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Mikaël Salson authored
Relative path is less robust when changing directory.
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- 11 Mar, 2015 8 commits
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Mathieu Giraud authored
These informations are not so easy to parse... but at leastthey are here.
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Mathieu Giraud authored
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Mathieu Giraud authored
As k-mers with extended nucleotides are now ignored, the count of k-mers in '-c germline' has slightly changed (< 0.05% variation in 'stanford-germlines.should_get'). There are also slight changes in the number of windows found in 'stanford-w100.should_get'.
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Mathieu Giraud authored
The challenging sequence isolated in 1f12079d gives now the same window when it is reversed-complemented. There was probably a 'N' in some IGHV germline.
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Mathieu Giraud authored
There are some 'N' and other extended nucleotides in the germline sequences. As we store in the indexes both the k-mers and their reverse complement, and as we handle extended nucleotides almost randomly (see tools:nuc_to_int()), we may have slight differences when analyzing some reads and their reverse complement. Ignoring such k-mers allow thus to be more deterministic, getting the same results on a (pure ACGT) read and its reverse complement. Another option (harder to implement) could be to add several k-mers in the index, but this would decrease the effective weight of the seed. Note that we should also improve the analysis of reads that includes extended nucleotides.
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Mathieu Giraud authored
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Mathieu Giraud authored
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Mathieu Giraud authored
This should change nothing, we should never go to the '?'.
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