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