#!/bin/bash

set -e
set -u

# Hyperfine parameters
# Locally, just run a handful of times per test
# but in the cloud, boost it to ten
num_runs=100 
# How many times to multiply the four reads file to make a large one
multiplier=1000
if [[ ! -z ${CI+x} ]]; then
  num_runs=1000
  multiplier=10000;
fi

if [[ -z ${thisDir+x} ]]; then
  echo "ERROR: \$thisDir needs to be set up in a shell script, and then this library should be sourced."
  exit 1
fi

# output directory for markdown files
reportsDir="$thisDir/hyperfine"
mkdir -pv $reportsDir

R1="$thisDir/../testdata/R1.fastq"
R2="$thisDir/../testdata/R2.fastq"

large_R1="$thisDir/../testdata/R1.large.fastq"
large_R2="$thisDir/../testdata/R2.large.fastq"

large_interleaved="$thisDir/../testdata/shuffled.large.fastq.gz"
large_sorted="$thisDir/../testdata/shuffled.sorted.fastq.gz"

R1_content=`cat $R1`;
R2_content=`cat $R2`;
for i in `seq 1 $multiplier`; do 
  echo "$R1_content"
done | seqkit rename > $large_R1
for i in `seq 1 $multiplier`; do 
  echo "$R2_content"
done | seqkit rename > $large_R2

# Save this file even though it's not used in the first benchmark
cat $R1 $R2 | fasten_shuffle | gzip -c9 > $large_interleaved
#ls -lhS $large_interleaved $R1 $R2

# Fasten sort file size
zcat $large_interleaved | fasten_sort --sort-by GC --paired-end | gzip -c > $large_sorted
#ls -lh $large_interleaved $large_sorted

which bbnorm.sh
which fasten_clean
which seqfu

# Version information
seqtk 2>&1 | grep -i version | sed 's/^/seqtk /'
seqkit version | grep -m 1 v
fasten_clean --version
fastq_to_fasta -h | grep "Part of FASTX"
bbnorm.sh version 2>&1 | grep 'BBMap version'
seqfu --version

# hyperfine
which hyperfine
which plot_whisker.py || echo "WARNING: plot_whisker.py from hyperfine not found in path: will not be able to plot graphs."