#!/bin/bash
set -eu

case $1 in
	--help)
		cat <<EOF
Usage: abyss-bowtie [OPTION]... QUERY... TARGET
Align the sequences of the files QUERY to those of the file
TARGET using bowtie.
EOF
		exit
		;;
	--version)
		cat <<EOF
abyss-bowtie (ABySS)
Written by Shaun Jackman.

EOF
		bowtie --version
		exit
		;;
esac

# Parse the command line.
bowtie='bowtie -S'
while getopts :j:l:v opt; do
	case $opt in
		j) bowtie="$bowtie -p$OPTARG";;
		l) ;;
		v) ;;
		\?) echo >&2 "abyss-bowtie: invalid option: $OPTARG"; exit 1;;
	esac
done
shift $((OPTIND-1))

query=("$@")
target=${query[${#query[@]}-1]}
unset query[${#query[@]}-1]
index=$target.1.ebwt

# Build the index.
if [ ! -r $index ]; then
	echo >&2 "Building the index $index..."
	echo >&2 bowtie-build $target $target
	bowtie-build $target $target 1>&2
elif [ $index -ot $target ]; then
	echo >&2 "The index $index is stale. Rebuilding the index..."
	echo >&2 bowtie-build $target $target
	bowtie-build $target $target 1>&2
else
	echo >&2 "The index $index is up to date."
fi

# Map the reads.
echo >&2 $bowtie $target "${query[@]}"
exec abyss-tofastq -i "${query[@]}" |$bowtie $target -
