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jts / sga

de novo sequence assembler using string graphs
http://genome.cshlp.org/content/22/3/549
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Kmer Count along a sequence (kmer-plot) #87

Closed jgurtowski closed 9 years ago

jgurtowski commented 9 years ago

For a particular input sequence, output the kmer counts from one or more bwt's.

Useful if you want to see the kmer coverage over a specific sequence.

In spirit of Amos kmer-cov-plot

jts commented 9 years ago

Thanks for this James, it looks great. I'll try to review and merge it in the next day or two.

jts commented 9 years ago

I didn't notice that the traversal algorithm was removed in the last commit so I've removed the comments specific to this code.

I have some nit-picky formatting comments - the file currently switches between in-line bracing and newline + brace. Can you standardize this? Probably best to use newline + brace since this is what the rest of SGA uses and I'd like to be consistent. Thanks!

jgurtowski commented 9 years ago

Kmer-count now can take a sequence file (kmer-plot functionality has been merged).

jts commented 9 years ago

Merged, thanks James!