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gmarcais / Jellyfish

A fast multi-threaded k-mer counter
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jellyfish count database format #104

Closed rfm-targa closed 6 years ago

rfm-targa commented 6 years ago

Greetings,

I'm working in taxonomic classification and a program I'm using uses Jellyfish 1. The program doesn't support Jellyfish 2 and I think it's because the output file of the count function has changed from Jellyfish 1 to 2. Could anyone tell me what exactly changed in the output of the count function? Is it possible to make the count function output of Jellyfish 2 equal to that of Jellyfish 1?

Thanks in advance!

gmarcais commented 6 years ago

The main change is in the header. The header of JF1 was binary and fixed length. The header of JF2 is in json and variable length. The rest should be the same, provided the k-mer length is below 31 bits.

There is no command provided right now to change the format from one to the other.

rfm-targa commented 6 years ago

Thank you very much for the reply, this helps.