Closes #3418.

See #3418.

feature-a/3393-binreadstorage-use-bins-when-necessary into dev

Closes #3393 and #3395

See merge request !267

Feature a/update TODOs

See merge request !257

Fixes #3395

Cyprien Borée authored Jul 27, 2018 and Mikaël Salson committed Jul 28, 2018

See #3393

See #3393

Cyprien Borée authored Jul 27, 2018 and Mikaël Salson committed Jul 28, 2018

Will be called when not all the reads can be stored.

Cyprien Borée authored Jul 27, 2018 and Mikaël Salson committed Jul 28, 2018

See #3393

This will help to reuse those functions elsewhere in the code

See #3393

Ryan Herbert authored Jul 18, 2018 and Mikaël Salson committed Jul 26, 2018

it matches what the scheduler would use. But we still need to check for
"DONE" since it currently exists in the database.

Ryan Herbert authored Jul 17, 2018 and Mikaël Salson committed Jul 26, 2018

It would seem that we use "DONE" to indicate a pre_process has
completed rather than "COMPLETED" as for scheduler tasks.

Feature s/update accesible sequence files

See merge request !265

models/sequence_file.py: Deal with either patient/run or sample_set for get_accessible_sequence_files_in_set_type

Features for CloneDB

Closes #2929 and #2311

See merge request !264

This was not the case when all the values were undefined (as with cloneDB occurrences).
We need just two labels, when with 0 and the other one with undefined.

computeSteps() had no effect has it was returned in an unused variable.

The nb_steps+1 is removed as it increments (for what reason?) the number of steps.

Follows d4398f13

min can be defined while max can be undefined

Alexia Omietanski authored Jul 26, 2018 and Mikaël Salson committed Jul 26, 2018

Fixes #2311

Alexia Omietanski authored Jul 26, 2018 and Mikaël Salson committed Jul 26, 2018

Fixes #2929

Fix FASTA export

Closes #1899 and #3417

See merge request !260

Fix #1899

The previous method was not robust enough because in  we can have
names such as TRGJ+down. This is not the case in m.germline where the names
are on 3 letters.
Moreover the code is now more generic.

Fix #3417

Display diversity with retro-compatibility

Closes #3416

See merge request !259

Diversity is now output under an Array by  (see #1941) but
this was not the case previously. We deal with both possibilities.

Fixes #3416

Don't know why and since when (see should#20)

See #3414.

From #2549

What was tested was not output anymore by fuse.py.
This replaces the test with something somewhat similar that is now output.
That also ensure the distribution is slightly tested.

The sequence is now correctly found as TRG.

Was useful for vdj696

fix queued jobs

See merge request !256

(cherry picked from commit 711c754f)

3dc5bccb task.py: DONE also exists

From #2549