From fb7f5d246f99bb2efd597d76a634866f4d3ab3d9 Mon Sep 17 00:00:00 2001 From: "Documenter.jl" Date: Wed, 6 Mar 2024 11:19:08 +0000 Subject: [PATCH] build based on 4df48b9 --- dev/.documenter-siteinfo.json | 2 +- dev/index.html | 2 +- dev/kmer_count_matrix/index.html | 2 +- dev/kmer_count_vector/index.html | 2 +- dev/kmer_int_repr/index.html | 2 +- dev/references/index.html | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/dev/.documenter-siteinfo.json b/dev/.documenter-siteinfo.json index aeeecde..2cf9a0f 100644 --- a/dev/.documenter-siteinfo.json +++ b/dev/.documenter-siteinfo.json @@ -1 +1 @@ -{"documenter":{"julia_version":"1.10.2","generation_timestamp":"2024-03-06T09:51:08","documenter_version":"1.3.0"}} \ No newline at end of file +{"documenter":{"julia_version":"1.10.2","generation_timestamp":"2024-03-06T11:19:05","documenter_version":"1.3.0"}} \ No newline at end of file diff --git a/dev/index.html b/dev/index.html index ce8b5ff..40d8cc5 100644 --- a/dev/index.html +++ b/dev/index.html @@ -1,2 +1,2 @@ -Home · VectorizedKmers.jl
GitHub

VectorizedKmers

Latest Release MIT license Documentation Documentation Status Coverage

VectorizedKmers.jl is a Julia package for fast $k$-mer counting of biological sequences. The core idea is that $k$-mers with an alphabet size $S$ are essentially integers in base $S$, and can be used as indices in a vector of size $S^k$ to count the corresponding $k$-mers.

The KmerVector type is a wrapper for AbstractVector, which means that these vector k-mer counts are not limited to Julia's Base.Vector type; other kinds of vectors can be used as well, such as CUDA.CuVector, SparseArrays.SparseVector or even matrix views.

To efficiently group k-mer counts together, the AbstractKmerMatrix stores them in a matrix as rows or columns. It can wrap any AbstractMatrix, such as Matrix or CuMatrix, and accessing its elements by index returns a KmerVector wrapped around a view of a row or column of the original matrix.

This data structure can be used to quickly approximate distances between sequences. Most notably, the squared Euclidean distance was used to approximate edit distance in this paper. The dot product has also proven to be a useful metric for comparing correlation between sequences.

Installation

You can install VectorizedKmers in your environment from the Julia REPL by entering pkg mode with ] and then running:

add VectorizedKmers
+Home · VectorizedKmers.jl
GitHub

VectorizedKmers

Latest Release MIT license Documentation Documentation Status Coverage

VectorizedKmers.jl is a Julia package for fast $k$-mer counting of biological sequences. The core idea is that $k$-mers with an alphabet size $S$ are essentially integers in base $S$, and can be used as indices in a vector of size $S^k$ to count the corresponding $k$-mers.

The KmerVector type is a wrapper for AbstractVector, which means that these vector k-mer counts are not limited to Julia's Base.Vector type; other kinds of vectors can be used as well, such as CUDA.CuVector, SparseArrays.SparseVector or even matrix views.

To efficiently group k-mer counts together, the AbstractKmerMatrix stores them in a matrix as rows or columns. It can wrap any AbstractMatrix, such as Matrix or CuMatrix, and accessing its elements by index returns a KmerVector wrapped around a view of a row or column of the original matrix.

This data structure can be used to quickly approximate distances between sequences. Most notably, the squared Euclidean distance was used to approximate edit distance in this paper. The dot product has also proven to be a useful metric for comparing correlation between sequences.

Installation

You can install VectorizedKmers in your environment from the Julia REPL by entering pkg mode with ] and then running:

add VectorizedKmers
diff --git a/dev/kmer_count_matrix/index.html b/dev/kmer_count_matrix/index.html index 2540c2e..5e286d1 100644 --- a/dev/kmer_count_matrix/index.html +++ b/dev/kmer_count_matrix/index.html @@ -31,4 +31,4 @@ 3 1 2 1 1 0 1 1 0 - 2 1 2 + 2 1 2 diff --git a/dev/kmer_count_vector/index.html b/dev/kmer_count_vector/index.html index 9a97b2b..6f1d0b9 100644 --- a/dev/kmer_count_vector/index.html +++ b/dev/kmer_count_vector/index.html @@ -27,4 +27,4 @@ 1 2 -julia> kv == kv2 +julia> kv == kv2 diff --git a/dev/kmer_int_repr/index.html b/dev/kmer_int_repr/index.html index ddca0a2..2dcc184 100644 --- a/dev/kmer_int_repr/index.html +++ b/dev/kmer_int_repr/index.html @@ -33,4 +33,4 @@ end kmer_int end

To test it, we can use the aa"..." string macro to create a LongAA instance:

julia> kmer_to_int(aa"AMINO")
-270556
+270556 diff --git a/dev/references/index.html b/dev/references/index.html index 87ca959..322e48d 100644 --- a/dev/references/index.html +++ b/dev/references/index.html @@ -1,2 +1,2 @@ -API Reference · VectorizedKmers.jl
GitHub
+API Reference · VectorizedKmers.jl
GitHub