1#!/usr/local/bin/bash
2
3usage(){
4echo "
5Written by Brian Bushnell
6Last modified May 2, 2017
7
8Description:  Remove Smart Bell adapters from PacBio reads.
9
10Usage:        removesmartbell in=<input> out=<output> split=t
11
12Input may be fasta or fastq, compressed or uncompressed (not H5 files).
13
14Parameters:
15in=file         Specify the input file, or stdin.
16out=file        Specify the output file, or stdout.
17adapter=        Specify the adapter sequence (default is normal SmrtBell).
18split=t            t: Splits reads at adapters.
19                   f: Masks adapters with X symbols.
20
21Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
22"
23}
24
25#This block allows symlinked shellscripts to correctly set classpath.
26pushd . > /dev/null
27DIR="${BASH_SOURCE[0]}"
28while [ -h "$DIR" ]; do
29  cd "$(dirname "$DIR")"
30  DIR="$(readlink "$(basename "$DIR")")"
31done
32cd "$(dirname "$DIR")"
33DIR="$(pwd)/"
34popd > /dev/null
35
36#DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
37CP="$DIR""current/"
38
39z="-Xmx400m"
40set=0
41
42if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
43	usage
44	exit
45fi
46
47calcXmx () {
48	source "$DIR""/calcmem.sh"
49	setEnvironment
50	parseXmx "$@"
51}
52calcXmx "$@"
53
54removesmartbell() {
55	local CMD="java $EA $EOOM $z -cp $CP pacbio.RemoveAdapters2 $@"
56	echo $CMD >&2
57	eval $CMD
58}
59
60removesmartbell "$@"
61