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Since 353497b7, both seq2 and seq4 are taken into account into this representative quality computation.

Mathieu Giraud authored Aug 04, 2016 and Vidjil Team committed Aug 04, 2016

This column provide direct links to results.

A new feature by @duez: we can now report the average quality in the representative sequence
of each clone. The quality is computed over Vidjil's window, shared between all reads of the clone.

core/representative.cpp: do not stop representative computation to correctly compute average quality

This commit may affect the global execution time.

This already existing bug was revealed by the tests.

Especially with RNAseq data, one may want to output reads with V/J similarities,
but not random reads for other parts of the genome.
The new behavior of the '-u' option is to return these interesting reads.

This is quadratic, both in time and in space in the .vidjil output.

This may lead to segmentation errors.

This is quadratic, both in time and in space in the .vidjil output.

Mathieu Giraud authored Aug 02, 2016 and Vidjil Team committed Aug 02, 2016

The Vidjil Morning failed sometimes.

This is our user manual. We do not mention 'browser' anywhere in this documentation except while referring to web browsers.

Some information was scattered in the previous organization.
This file is now the central place to store *developer* information.
We may one day re-split this documentation into several files.

Some external tools would like to provide sequence features with textual information.
Discussion with @flothoni and @duez.

'stop' positions are included in the highlight (5e21e0).