#!/bin/bash
set -eu

case $1 in
	--help)
		cat <<EOF
Usage: abyss-bwasw [OPTION]... QUERY... TARGET
Align the sequences of the files QUERY to those of the file
TARGET using bwa.
EOF
		exit
		;;
	--version)
		cat <<EOF
abyss-bwasw (ABySS)
Written by Shaun Jackman.
EOF
		bwa 2>&1 |head -n4
		exit
		;;
esac

# Parse the command line.
bwasw='bwa bwasw'
bwa_index='bwa index -a bwtsw'
while getopts :j:l:v opt; do
	case $opt in
		j) bwasw="$bwasw -t$OPTARG";;
		l) ;;
		v) ;;
		\?) echo >&2 "abyss-bwasw: invalid option: $OPTARG"; exit 1;;
	esac
done
shift $((OPTIND-1))

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

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

# Map the reads.
echo >&2 $bwasw $target "${query[@]}"
exec abyss-tofastq -i "${query[@]}" \
	|$bwasw $target - \
	|awk '
BEGIN {
	OFS = "\t"
}
/^@/ { print; next }
$1 == x { next }
{ x = $1 }
sub("/1$", "", $1) > 0 {
	$2 = or($2, 0x41)
	print; next
}
sub("/[23]$", "", $1) > 0 {
	$2 = or($2, 0x81)
	print; next
}
{ print }
'