#!/usr/bin/env bash
#
# Sweeps through the bowtie2 parameters space.
#
# Based on a script by Fan Song.
#
# Usage:
#
#	bash bowtie2-parameter-sweep.sh
#
# or to set an error rate of 10%
#
# 	bash bowtie2-parameter-sweep.sh 0.1
#
#
set -ue

# Default value for the script.
ERR=${1:-0.02}

# Make a directory
mkdir -p temp

# This will be the reference.
REF=temp/GENOME.fa

# Get the data
echo "# Getting a reference"
efetch -db=nuccore -format=fasta -id=AF086833 > $REF

# Build an index from the genome.
echo "# Building the index"
bowtie2-build $REF $REF > temp/log1  2>> temp/log2

# Generate a simulated genome.
echo "# Simulating a genome with error rate=$ERR"
wgsim -N 10000 -e $ERR $REF R1.fq R2.fq > temp/log1  2>> temp/log2

# Set read names.
R1=R1.fq
R2=R2.fq

# Generate parameter sweep.
printf "Concord\tDiscord\tOneTime\tParams\n"
for D in {5..15}; do
for R in {1..3}; do
for N in {0..1}; do
for L in {15..25}; do
for i1 in {0..1}; do
for i2 in `seq 0.5 0.25 2.5`; do
bowtie2 -x $REF -1 $R1 -2 $R2 -S output.sam -D $D -R $R -N $N -L $L -i S,${i1},${i2} 2> tmp
conc=`grep "aligned concordantly exactly 1 time" tmp | awk '{print $1}'`
disc=`grep "aligned discordantly 1 time" tmp | awk '{print $1}'`
onet=`grep "aligned exactly 1 time" tmp | awk '{print $1}'`
printf "%d\t%d\t%d\t(%d,%d,%d,%d,%d,%.2f)\n"  $conc $disc $onet $D $R $N $L $i1 $i2
done
done
done
done
done
done