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Find all significant local alignments between reads
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Identify (-I) flag in HPC.daligner #53

Closed gt1 closed 7 years ago

gt1 commented 7 years ago

daligner has the -I flag for computing alignments between a read and itself. This flag is missing in HPC.daligner. I think it would be useful to have it in HPC.daligner as well.

thegenemyers commented 7 years ago

It was there but I took it out once I generalized HPC.daligner to do a data set against itself, and to do a data set against another. I think of HPC.daligner as a script generator for these instances, in which case -I doesn't make sense.

-I is really only useful if you are looking for tandems or internal structure. HPC.tandem does that better.

-- Gene

On 12/7/16, 12:26 PM, German Tischler wrote:

daligner has the -I flag for computing alignments between a read and itself. This flag is missing in HPC.daligner. I think it would be useful to have it in HPC.daligner as well.

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