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thegenemyers / DALIGNER

Find all significant local alignments between reads
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HPC.daligner -d option cleanup #59

Closed gt1 closed 7 years ago

gt1 commented 7 years ago

Using the -d option of HPC.daligner the program outputs a section containing sequences like

cd dir rm files cd ..

which is not consistent with the semantics that every line of a section can be executed in parallel to get the same result as when running the lines sequentially.

I would suggest to replace this by

cd dir ; rm files ; cd ..

thegenemyers commented 7 years ago

I assumed one would never execute that section on the cluster, but rather serially on the file server. But you are right in that in so doing I abandoned a property I had asserted in the documentation. So I changed it as per your suggestion, so the property remains true. Thanks, Gene

On 4/6/17, 10:45 AM, German Tischler wrote:

Using the -d option of HPC.daligner the program outputs a section containing sequences like

cd dir rm files cd ..

which is not consistent with the semantics that every line of a section can be executed in parallel to get the same result as when running the lines sequentially.

I would suggest to replace this by

cd dir ; rm files ; cd ..

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