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dib-lab / khmer

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
http://khmer.readthedocs.io/
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Refine disk space checks #618

Open RamRS opened 10 years ago

RamRS commented 10 years ago

The current algorithm that checks disk space before writing output makes the following assumptions:

  1. No output file can be larger in size than the largest input file
  2. Input and output files will be stored in the same disk
  3. There is no provision to bypass a space check (part of https://github.com/ged-lab/khmer/issues/399)

There may also be other issues with the current approach, that we can add as we discover. We discuss possible alternative approaches and tweaks in this thread.

mr-c commented 9 years ago

For example, normalize-by-median.py passes all of these except for #2

ctb commented 9 years ago

@mr-c, what needs to be done here? I'm confused. We've addressed most of this in #1170 and I think we can probably just close this, unless specific tasks can be identified.

mr-c commented 9 years ago