If no read was segmented we may encounter an error in that case

These *.py files should be moved to /tools

Link to #3943

link to #3943

This field should show a null value instead of 0 if not present
link to #3943

Fix #3833

should-vdj-to-tap.py could be moved to tools.

should@28eaf5a6
see #3762

should@2a21dfd9

- Define a function that could be used for post-processing
- Use defs.py to determine where the pre-process are stored
- Should tests

See #3647

Closes #3585.

See #3585.

See #3647.

should@8f711a78

link to #3054

link to 3054

link to #3054

link to #3054

With this script, we have the possibility to get structured datas from the pear preprocess to use them into the server, for quality, warning, ...
link to #3054 #3049 #3154

This will allow to more reliably add percentages that otherwise would give
meaningless results.

In the test we now have 497 reads out of 786861.

allows vidjil files to contain no clones

Fixes #2929

So that dependencies only need to be installed if VidjilParser is used.
Thanks @mikael-s :)

Being a fast parser allows us to gain a significant amount of time when
executing.

Restore old functionality and make new functionality optional.
Due to the amount of time it takes to run the vidjilparser we may need
to decide between speed and memory efficiency

See #3234

split VidjilWriter into VidjilWriter and VidjilFileWriter

use yajl2 as the ijson parser since it is much faster.

See #3234,#3235

use a list for the buffer and join strings when needed. This should be
slightly faster than concatenating strings.

due to the error in the prefix usage, we were extracting all clones from
the file instead of the top N, leading to horrendous performance issues.