From 571c86588559ed7f5c8c6ca913000ac213065d7e Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sat, 30 Sep 2023 07:07:45 -0700 Subject: [PATCH] minor corrections --- doc/faq.md | 2 +- doc/sourmash-internals.md | 26 +++++++++++++------------- 2 files changed, 14 insertions(+), 14 deletions(-) diff --git a/doc/faq.md b/doc/faq.md index 0be10ca51e..2f1e0fecd6 100644 --- a/doc/faq.md +++ b/doc/faq.md @@ -217,7 +217,7 @@ matching genome. ## Can I use sourmash to determine the best reference genome for mapping my reads? Yes! (And see the FAQ above, -[How do k-mer analyses compare with read mapping?](#how-do-k-mer-based-analyses-compare-with-read-mapping).) +[How do k-mer analyses compare with read mapping?](#how-do-k-mer-based-analyses-compare-with-read-mapping)) If you're interested in picking a single best reference genome (from a large database) for read mapping, you can do the following: diff --git a/doc/sourmash-internals.md b/doc/sourmash-internals.md index 2799f21a4e..6aaeee90e5 100644 --- a/doc/sourmash-internals.md +++ b/doc/sourmash-internals.md @@ -647,24 +647,24 @@ n+1 problem Since `sourmash gather` will pick only one "best match" if there are several (and will ignore the others), the order of searching -can matter for multiple collections. How does this work? +can matter for large collections. How does this work? In brief, sourmash doesn't guarantee a particular load order for sketches in a single collection, but it _does_ guarantee that collections are loaded and searched in their entirety in the order that you provide them. So, for example, if you have a large zipfile -database of sketches that contain some duplicates, you can't pick -which of the duplicates will be chosen as a match; but you _can_ -provide your own collection of prioritized matches as a separate -database. A practical application of this might be to provide the -GTDB "representatives" database first on the command line, with the -full GTDB database second, in order to prioritize choosing -representative genomes as matches over the rest. - -This also plays a role in the order of reporting for `prefetch` - -`prefetch` will report matching sketches in the order it encounters -them, which will match the order in which collections are given -to `sourmash prefetch` on the command line. +database of sketches that contains duplicates, you can't predict which +of the duplicates will be chosen as a match; but you _can_ build your +own collection of prioritized matches as a separate database, and put +it first on the command line. A practical application of this might +be to list the GTDB "representatives" database first on the command +line, with the full GTDB database second, in order to prioritize +choosing representative genomes as matches over the rest. + +This also plays a role in the order of reporting for `prefetch` +output - `prefetch` will report matching sketches in the order it +encounters them, which will match the order in which collections are +given to `sourmash prefetch` on the command line. ## Formats natively understood by sourmash