search

AliTVTeam / AliTV

Visualize whole genome alignments as linear maps
https://alitvteam.github.io/AliTV/d3/AliTV.html
MIT License
69 stars 11 forks source link

Message on sequence length #185

Open krostifangers opened 1 year ago

krostifangers commented 1 year ago

Hello I have the following message at the end of AliTV analysis : INFO - Number of bases (32288313) is longer than the maximum allowed (1000000), therefore sequences will be excluded from JSON file I tried to compare the first chromosome of six genomes of a fungus. Each chromosome is about 5-6Mb long. I used maf pairwise alignments performed with minimap2. The figure seems correct, so I want to understand this message. Thank you in advance C Lemaire

iimog commented 1 year ago

Hi C Lemaire,

you don't have to worry about this message.

The default behavior of AliTV is to store the genomic sequences in the generated json file. In order to reduce the size of these json files, they are not saved if the sequences are too long (exceeding 1Mbp).

We added sequences, because we planned to implement zooming down to the base pair level. However, this is not implemented, yet. Currently, the AliTV web interface, does not use the sequences at all. So it does not matter whether the json contains them or not.

As our plans to implement any features using the sequences are on hold, it might be best to never write sequences to the json and drop this message. What do you think @greatfireball?

Best, Markus