GitLab

See vdj#512.

Fix report generation with one sample

See merge request !144

1724 SEG_METHOD_ONE: mapping non-recombined reads

See merge request !75

The graph is not always used in the report.
I don't know the reason why the graph was used here but
it seems that is was sometimes not working well with double
scatterplots

Sources given by @magiraud in #2957

See #2954

Since vdj#42d776e5

See #XXXX.

This should look less hacky than what was in 31581d71.
See #XXXX.

A more flexible and explicit method of selecting the target field for
foreign_key replacement.
Appending "_id" to the table name (stored as the key for the mapping)
does not work for al situations, especially if managing table that were
not created for the current application, so explicitly mapping the
mapping key to the target field will be more flexible.

log was attempting to use undefined variable

the mapping file requires the keys to be strings, which was causing
the import to fail to recognise that a missing config was present in the
config. Casting the string properties to longs allows proper use of the
cofig mapper.

also copies results, fused and analysis files

Feature a+c/2247 warnings

Closes #2917

See merge request !139

See #1724.

See #1724.

See #1801.

CD.fa may be too large and fill the indexes.

See #1724.

See #1724.

This is somewhat hacky and could be changed by something more explicit.
See #1724.

This is evil. Vidjil was designed to handle recombinations,
not to be a read mapper. See #1724.

Moreover, we should extract a window in a more reproducible way.
See #2643.

See #2640.
Note that we use here a GenericAxis() instead of a GermlineAxis().
The 'D allele' can thus not implemented so easily now.

file.py fix duplicate file check

Closes #2855

See merge request !128

Remove default homopolymer cost

Closes #2851

See merge request !137

See #2917.

See #2917.

See #2916.

See #2916.

Feature c/enhance normalisation

Closes #2680, #2668, #2670, #2669, #2565, #2568, and #2681

See merge request !115

Feature c/2703 numeric axes clean

See merge request !138

Follows 5206c45d.

Follows 5206c45d.

Follows 5206c45d. See #2703.