Input from stdin about nonpareil HOT 2 OPEN

Hello @koopkaup
Unfortunately, that would require major changes in the code, because the input files are read multiple times:

• For -T kmer or -T alignment in one machine: There is an initial file pass to sample query reads and count total reads, and a second pass to run the comparisons.
• For -T alignment with MPI: Each machine makes a pass as opposed to sending data directly to worker nodes to reduce bandwidth use.

However, I think we could implement an option to read directly from zipped files (gzip / bzip2), what do you think @gunturus ?

M

from nonpareil.

For random sampling, we randomly move to a position in the file. So, this will require us to have the file uncompressed to begin with.

from nonpareil.