Large k value

Question

Large k value

Closed this issue 7 years ago · 8 comments

Hello !
I would be very interested to use TwoPaCo with large kmers.
It works with 281 but not with 291 on Ecoli reference genome.
./twopaco -f 30 -k 291 ../../../../data/ecoli.fa
Give a segfault.

Would it be possible for TwoPaCo to works on arbitray size of k ?

Answer 1 · 2017-03-29T15:45:44.000Z

Yes, it is possible. I updated the doc: https://github.com/medvedevgroup/TwoPaCo#k-mer-size

Answer 2 · 2017-03-29T16:04:16.000Z

In the next release I will make it a parameter for running CMake such that the user will be allowed to specify maximum K directly without editing the code.

Answer 3 · 2017-03-30T08:40:08.000Z

That would be the perfect solution.

Also do you think it would be possible for graphdump to have a regular fasta output option ?
It would be really convenient.

Excellent piece of work by the way !

Answer 4 · 2017-03-30T13:24:07.000Z

Thank you. You mean FASTA file with compressed paths? If so, it is not hard to do, I will add in the next release.

Answer 5 · 2017-03-30T15:16:55.000Z

Yes it would be great. Thank you for your answers

Answer 6 · 2017-05-18T20:41:12.000Z

Added in 0.9.2.

Answer 7 · 2017-05-18T21:26:22.000Z

I just tested it

graphdump -f fasta test.bin -s seq51.fa
PARSE ERROR: Argument: -f (--format)
Value 'fasta' does not meet constraint: seq|group|dot|gfa1|gfa2

Answer 8 · 2017-05-19T16:09:57.000Z

That is interesting. Are you sure you pulled the latest revision? What is the output of --help, does fasta appear in the formats list?