paper figures

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]]

paper/clean.json.png

@@ -0,0 +1 @@
+../tests/hyperfine/clean.json.png

paper/convertToFasta.json.png

@@ -0,0 +1 @@
+../tests/hyperfine/convertToFasta.json.png

paper/interleave.json.png

@@ -0,0 +1 @@
+../tests/hyperfine/interleave.json.png

paper/kmer.json.png

@@ -0,0 +1 @@
+../tests/hyperfine/kmer.json.png

paper/normalize.json.png

@@ -0,0 +1 @@
+../tests/hyperfine/normalize.json.png

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
 

paper/progress.json.png

@@ -0,0 +1 @@
+../tests/hyperfine/progress.json.png

paper/regex.json.png

@@ -0,0 +1 @@
+../tests/hyperfine/regex.json.png

paper/sample.json.png

@@ -0,0 +1 @@
+../tests/hyperfine/sample.json.png

paper/sort.json.png

@@ -0,0 +1 @@
+../tests/hyperfine/sort.json.png

paper/straighten.json.png

@@ -0,0 +1 @@
+../tests/hyperfine/straighten.json.png

paper/trim.json.png

@@ -0,0 +1 @@
+../tests/hyperfine/trim.json.png

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