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kbaseattic / assembly

An extensible framework for genome assembly.
MIT License
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bhammer module limitations #157

Open levinas opened 10 years ago

levinas commented 10 years ago
  1. For some reason, bhammer complaints about bz2 files while spades doesn't.
  2. The bhammer plugin currently doesn't support multiple paired-end libraries. Should copy the spades plugin code over.
cbun commented 10 years ago

I've been flip flopping on this for a while, but I think this might just be the way to do it. The idea is that preprocessing works individually on a library the same way as on multiple. This is not the case for assemblers.

You could imagine an expression like

(spades (bhammer READS1) READS2)

I think (bhammer READS) should of course do the right thing, but it may not be correct for the plug-in writer to expect to handle multiple libraries. Logic should be elsewhere. On Jul 12, 2014 5:34 PM, "Fangfang Xia" notifications@github.com wrote:

1.

For some reason, bhammer complaints about bz2 files while spades doesn't. 2.

The bhammer plugin currently doesn't support multiple paired-end libraries. Should copy the spades plugin code over.

— Reply to this email directly or view it on GitHub https://github.com/kbase/assembly/issues/157.

cbun commented 10 years ago

no.2 Fixed in 04e895bd3a73857db638d5007b3a2c396406d37a