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genotoul-bioinfo / dgenies

Dotplot large Genomes in an Interactive, Efficient and Simple way
http://dgenies.toulouse.inrae.fr
GNU General Public License v3.0
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Consider exposing "max_nb_lines" #16

Open tanghaibao opened 4 years ago

tanghaibao commented 4 years ago

Dear,

Thank you for the excellent plotting software.

The setting max_nb_lines controls how many highest scoring alignments to include in the dot plot, and is fixed in the source code to be 100000. For fragmented assemblies with numerous contigs, this value is grossly insufficient.

I would love to see this parameter exposed, either:

When I experimented with this parameter for this use case, I noticed that there are additional performance improvements necessary for the use case when lots of contigs are involved: https://github.com/genotoul-bioinfo/dgenies/pull/15

Haibao

pbordron commented 2 years ago

Exposed in config file in 1.3

pbordron commented 1 year ago

There is two way to working on a webform input box .

  1. Easy to do: send all data (with a max defined on the server side) and only display first ones.
  2. A bit more complicated: send first ones and have an additional route to ask more lines.

Solution [1] will consume more network resources (and user memory) than solution [2].