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Mikaël Salson authored Jun 22, 2015 and Vidjil Team committed Jun 22, 2015

Useful when we want all the values

Mikaël Salson authored Jun 22, 2015 and Vidjil Team committed Jun 22, 2015

controllers/patient.py: process in the same way all the maps retrieved from the result and fused files

Mikaël Salson authored Jun 22, 2015 and Vidjil Team committed Jun 22, 2015

The value is searched in the result file but regex are not very robust to slight changes in the output
(which could happen when… changing the JSON output library). Now we use JSON paths which should be more
robust.
The first clone has index 0 in Vidjil's output file.

Mikaël Salson authored Jun 22, 2015 and Vidjil Team committed Jun 22, 2015

Doing an index() on a list is more reliable than a find() on a string separated with _
as suggested by @magiraud.

Mikaël Salson authored Jun 22, 2015 and Vidjil Team committed Jun 22, 2015

sequence_file_list is not a reliable way of retrieving the corresponding fused files.
Instead we rely on the patient and config IDs and take the most recent files among
the corresponding fused files

Mikaël Salson authored Jun 18, 2015 and Vidjil Team committed Jun 18, 2015

This prevents an ambiguity because filter() is called in advanced_filter()

Mikaël Salson authored Jun 18, 2015 and Vidjil Team committed Jun 18, 2015

This prevents encoding issues between the different strings when they are concatenated

Instead of testing whether rep_4 is empty, we define
two different segmentation methods.

Selecting the segmentation method is now cleaner, and does
not require any string comparison. This allows to have (pseudo-)germlines with
the same locus but with different segmentation methods, as here
"xxx" for both MAX12 and MAX1U.

This experimental option tries to segment reads while detecting
translocations involving, for one part, the V(D)J region.

It works - but the probabilistic model is far too stringent here,
giving a p-value of about 0.1-0.2 for 40 unknown kmers.
Somehow, if one half of the read is in V(D)J, then having
unknown kmers in the other half is unexpected !

Now the e-value test is very stringent: we need a '-e 10'.

tests: tests .getIndexLoad() and .getProbability() with both AFFECT_UNKNOWN and AFFECT_NOT_UNKNOWN kmers

The e-value computation could be more precise by taking into account the actual kmer.

The very special germline PSEUDO_GERMLINE_MAX1U is similar to the PSEUDO_GERMLINE_MAX12 germline.

It uses the usual KmerSegmenter, but launches computeSegmentation()
on the most frequent KmerAffect of the read and on the unknown kmer, detecting
translocations involving, for one part, the V(D)J region.

-10 is when there is no rep4. Fix 928a98e6.