Mathieu Giraud authored Mar 16, 2015 and Vidjil Team committed Mar 16, 2015

This adds a 'format' optional argument to db.call('admin/log').

Mathieu Giraud authored Mar 16, 2015 and Vidjil Team committed Mar 16, 2015

We should use regexps here.

Mathieu Giraud authored Mar 14, 2015 and Vidjil Team committed Mar 14, 2015

Some <tr> rows shall not have cursor:pointer.

Mathieu Giraud authored Mar 14, 2015 and Vidjil Team committed Mar 14, 2015

The default call to XML() should be safe enough to prevent XSS attacks.

Mathieu Giraud authored Mar 14, 2015 and Vidjil Team committed Mar 14, 2015

It may be useful to inspect some data referred in a log.

remove tag from global var

Thanks to Paulo Alexandre Borges Miranda
http://stackoverflow.com/a/19595496/1192742

Makefile: Allow to launch a single functional test with valgrind by prefixing its name with valgrind_

This has no consequence since this rule is forced anyway.

Relative path is less robust when changing directory.

These informations are not so easy to parse... but at leastthey are here.

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'.

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.

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.

This should change nothing, we should never go to the '?'.