get_alignment: Added '-' as a viable base

rachelss / SISRS

Site Identification from Short Read Sequences.

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get_alignment: Added '-' as a viable base #39

Closed BobLiterman closed 7 years ago

BobLiterman commented 7 years ago

Just added '-' as a viable base to put into the final alignment, allowing us to treat gaps as characters assuming they fit other SISRS filtering criteria.

BobLiterman commented 7 years ago

I changed some script permissions which were set incorrectly (ie. my test script).

Also, I added a script which takes the renamed scaffolds and outputs a TSV file with scaffold lengths, which I will be using downstream for locus analysis.

rachelss commented 7 years ago

I think we should be merging from fork-develop to main-develop