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amplab / snap

Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data
https://www.microsoft.com/en-us/research/project/snap/
Apache License 2.0
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Documentation says default seed size is 27 but log and help say 24 #149

Closed eboyden closed 2 years ago

eboyden commented 2 years ago

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 2 years ago

The manual didn't get updated. We changed the default from 27 in 1.0 to 24 in 2.0.

From: eboyden @.> Sent: Thursday, January 6, 2022 9:30 PM To: amplab/snap @.> Cc: Subscribed @.***> Subject: [amplab/snap] Documentation says default seed size is 27 but log and help say 24 (Issue #149)

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 []

Options:

-s Seed size (default: 24)

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eboyden commented 2 years ago

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 2 years ago

Fixed in 2.0.1