From 4283af322c47bcbb53a5c9b7734fbbfb180b5644 Mon Sep 17 00:00:00 2001 From: Lee Katz - Aspen Date: Wed, 1 Nov 2023 12:30:42 -0400 Subject: [PATCH] paper figures --- Cargo.toml | 6 ++++-- paper/clean.json.png | 1 + paper/convertToFasta.json.png | 1 + paper/interleave.json.png | 1 + paper/kmer.json.png | 1 + paper/normalize.json.png | 1 + paper/paper.md | 18 +++++++++--------- paper/progress.json.png | 1 + paper/regex.json.png | 1 + paper/sample.json.png | 1 + paper/sort.json.png | 1 + paper/straighten.json.png | 1 + paper/trim.json.png | 1 + tests/lib/benchmark.sh | 2 +- 14 files changed, 25 insertions(+), 12 deletions(-) create mode 120000 paper/clean.json.png create mode 120000 paper/convertToFasta.json.png create mode 120000 paper/interleave.json.png create mode 120000 paper/kmer.json.png create mode 120000 paper/normalize.json.png create mode 120000 paper/progress.json.png create mode 120000 paper/regex.json.png create mode 120000 paper/sample.json.png create mode 120000 paper/sort.json.png create mode 120000 paper/straighten.json.png create mode 120000 paper/trim.json.png diff --git a/Cargo.toml b/Cargo.toml index 1c306f58..9adbf0ea 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -10,10 +10,12 @@ repository = "https://github.com/lskatz/fasten" categories = ["command-line-utilities", "science"] keywords = ["bioinformatics","fastq","streaming"] readme = "./README.md" -# Docs have been copied over for the purposes of github pages -# and should not be included in the package exclude = [ + # Docs have been copied over for the purposes of github pages + # and should not be included in the package "docs/*", + # Do not include the manuscript in the package + "paper/*", ] [[bin]] diff --git a/paper/clean.json.png b/paper/clean.json.png new file mode 120000 index 00000000..4c93ff2d --- /dev/null +++ b/paper/clean.json.png @@ -0,0 +1 @@ +../tests/hyperfine/clean.json.png \ No newline at end of file diff --git a/paper/convertToFasta.json.png b/paper/convertToFasta.json.png new file mode 120000 index 00000000..d56fd745 --- /dev/null +++ b/paper/convertToFasta.json.png @@ -0,0 +1 @@ +../tests/hyperfine/convertToFasta.json.png \ No newline at end of file diff --git a/paper/interleave.json.png b/paper/interleave.json.png new file mode 120000 index 00000000..cd3f9006 --- /dev/null +++ b/paper/interleave.json.png @@ -0,0 +1 @@ +../tests/hyperfine/interleave.json.png \ No newline at end of file diff --git a/paper/kmer.json.png b/paper/kmer.json.png new file mode 120000 index 00000000..e0f4453c --- /dev/null +++ b/paper/kmer.json.png @@ -0,0 +1 @@ +../tests/hyperfine/kmer.json.png \ No newline at end of file diff --git a/paper/normalize.json.png b/paper/normalize.json.png new file mode 120000 index 00000000..e5e227fc --- /dev/null +++ b/paper/normalize.json.png @@ -0,0 +1 @@ +../tests/hyperfine/normalize.json.png \ No newline at end of file diff --git a/paper/paper.md b/paper/paper.md index 152cd562..cf784dad 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -44,23 +44,23 @@ Benchmarking was performed against other mainstream packages using `hyperfine` u Documentation, the container, and code are available at GitHub. Benchmarking results were graphed into Figures \label{fig:clean} - \label{fig:straighten}. -![Trimming with a minimum quality score \label{fig:clean}](../tests/hyperfine/clean.json.png) +![Trimming with a minimum quality score \label{fig:clean}](clean.json.png) -![converting fastq to fasta \label{fig:convertToFasta}](../tests/hyperfine/convertToFasta.json.png) +![converting fastq to fasta \label{fig:convertToFasta}](convertToFasta.json.png) -![interleaving R1 and R2 reads \label{fig:interleave}](../tests/hyperfine/interleave.json.png) +![interleaving R1 and R2 reads \label{fig:interleave}](interleave.json.png) -![kmer counting \label{fig:kmer}](../tests/hyperfine/kmer.json.png) +![kmer counting \label{fig:kmer}](kmer.json.png) -![normalizing read depth using kmer coverage \label{fig:normalize}](../tests/hyperfine/normalize.json.png) +![normalizing read depth using kmer coverage \label{fig:normalize}](normalize.json.png) -![Searching for a sequence in a fastq file \label{fig:regex}](../tests/hyperfine/regex.json.png) +![Searching for a sequence in a fastq file \label{fig:regex}](regex.json.png) -![downsampling reads \label{fig:sample}](../tests/hyperfine/sample.json.png) +![downsampling reads \label{fig:sample}](sample.json.png) -![sorting fastq entries by either sequence or ID \label{fig:sort}](../tests/hyperfine/sort.json.png) +![sorting fastq entries by either sequence or ID \label{fig:sort}](sort.json.png) -![converting nonstandard fastq files to a format whose entries are four lines each, and selecting the first 100 \label{fig:straighten}](../tests/hyperfine/straighten.json.png) +![converting nonstandard fastq files to a format whose entries are four lines each, and selecting the first 100 \label{fig:straighten}](straighten.json.png) ## Conclusions diff --git a/paper/progress.json.png b/paper/progress.json.png new file mode 120000 index 00000000..0bc134df --- /dev/null +++ b/paper/progress.json.png @@ -0,0 +1 @@ +../tests/hyperfine/progress.json.png \ No newline at end of file diff --git a/paper/regex.json.png b/paper/regex.json.png new file mode 120000 index 00000000..16f98a8a --- /dev/null +++ b/paper/regex.json.png @@ -0,0 +1 @@ +../tests/hyperfine/regex.json.png \ No newline at end of file diff --git a/paper/sample.json.png b/paper/sample.json.png new file mode 120000 index 00000000..abde7623 --- /dev/null +++ b/paper/sample.json.png @@ -0,0 +1 @@ +../tests/hyperfine/sample.json.png \ No newline at end of file diff --git a/paper/sort.json.png b/paper/sort.json.png new file mode 120000 index 00000000..dac365dc --- /dev/null +++ b/paper/sort.json.png @@ -0,0 +1 @@ +../tests/hyperfine/sort.json.png \ No newline at end of file diff --git a/paper/straighten.json.png b/paper/straighten.json.png new file mode 120000 index 00000000..b366fa83 --- /dev/null +++ b/paper/straighten.json.png @@ -0,0 +1 @@ +../tests/hyperfine/straighten.json.png \ No newline at end of file diff --git a/paper/trim.json.png b/paper/trim.json.png new file mode 120000 index 00000000..000d6b4b --- /dev/null +++ b/paper/trim.json.png @@ -0,0 +1 @@ +../tests/hyperfine/trim.json.png \ No newline at end of file diff --git a/tests/lib/benchmark.sh b/tests/lib/benchmark.sh index ca593510..5314d815 100644 --- a/tests/lib/benchmark.sh +++ b/tests/lib/benchmark.sh @@ -6,7 +6,7 @@ set -u # Hyperfine parameters # Locally, just run a handful of times per test # but in the cloud, boost it to ten -num_runs=20 +num_runs=100 # How many times to multiply the four reads file to make a large one multiplier=1000 if [[ ! -z ${CI+x} ]]; then