amplab/snap

Documentation says default seed size is 27 but log and help say 24

eboyden opened this issue · 3 comments

eboyden commented

Using SNAP 2.0.0. Both the long manual and the quick start guide say the default seed size is 27. But using default indexing parameters, the aligner log file shows:

Welcome to SNAP version 2.0.0.

Loading index from directory... 25s.  3110877063 bases, seed size 24
Aligning.

And the index command help message says:

/tools/snap/v2.0.0/snap-aligner index
Welcome to SNAP version 2.0.0.

Usage: snap-aligner index <input.fa> <output-dir> [<options>]
Options:
 -s                Seed size (default: 24)
bolosky commented
eboyden commented

Yup I figured that's what happened. Just letting you know the documentation needs updating.

And BTW, I really appreciate how well-documented this software is - I wish all binfx software developers followed this example.

bolosky commented

Fixed in 2.0.1