jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Brian Bushnell
jpayne@69: Last modified May 23, 2016
jpayne@69: 
jpayne@69: Description:  Replaces read names with names from another file.
jpayne@69: The other file can either be sequences or simply names, with
jpayne@69: one name per line (and no > or @ symbols).  If you use one name
jpayne@69: per line, please give the file a .header extension.
jpayne@69: 
jpayne@69: Usage:  replaceheaders.sh in=<file> hin=<headers file> out=<out file>
jpayne@69: 
jpayne@69: Parameters:
jpayne@69: in=                 Input sequences.  Use in2 for a second paired file.
jpayne@69: in=                 Header input sequences.  Use hin2 for a second paired file.
jpayne@69: out=                Output sequences.  Use out2 for a second paired file.
jpayne@69: ow=f                (overwrite) Overwrites files that already exist.
jpayne@69: zl=4                (ziplevel) Set compression level, 1 (low) to 9 (max).
jpayne@69: int=f               (interleaved) Determines whether INPUT file is considered interleaved.
jpayne@69: fastawrap=70        Length of lines in fasta output.
jpayne@69: qin=auto            ASCII offset for input quality.  May be 33 (Sanger), 64 (Illumina), or auto.
jpayne@69: qout=auto           ASCII offset for output quality.  May be 33 (Sanger), 64 (Illumina), or auto (same as input).
jpayne@69: 
jpayne@69: Renaming modes (if not default):
jpayne@69: addprefix=f         Rename the read by prepending the new name to the existing name.
jpayne@69: 
jpayne@69: Sampling parameters:
jpayne@69: reads=-1            Set to a positive number to only process this many INPUT reads (or pairs), then quit.
jpayne@69: 
jpayne@69: Java Parameters:
jpayne@69: -Xmx                This will set Java's memory usage, overriding autodetection.
jpayne@69:                     -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
jpayne@69:                     The max is typically 85% of physical memory.
jpayne@69: -eoom               This flag will cause the process to exit if an
jpayne@69:                     out-of-memory exception occurs.  Requires Java 8u92+.
jpayne@69: -da                 Disable assertions.
jpayne@69: 
jpayne@69: Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
jpayne@69: "
jpayne@69: }
jpayne@69: 
jpayne@69: #This block allows symlinked shellscripts to correctly set classpath.
jpayne@69: pushd . > /dev/null
jpayne@69: DIR="${BASH_SOURCE[0]}"
jpayne@69: while [ -h "$DIR" ]; do
jpayne@69:   cd "$(dirname "$DIR")"
jpayne@69:   DIR="$(readlink "$(basename "$DIR")")"
jpayne@69: done
jpayne@69: cd "$(dirname "$DIR")"
jpayne@69: DIR="$(pwd)/"
jpayne@69: popd > /dev/null
jpayne@69: 
jpayne@69: #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
jpayne@69: CP="$DIR""current/"
jpayne@69: 
jpayne@69: z="-Xmx1g"
jpayne@69: set=0
jpayne@69: 
jpayne@69: if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
jpayne@69: 	usage
jpayne@69: 	exit
jpayne@69: fi
jpayne@69: 
jpayne@69: calcXmx () {
jpayne@69: 	source "$DIR""/calcmem.sh"
jpayne@69: 	setEnvironment
jpayne@69: 	parseXmx "$@"
jpayne@69: }
jpayne@69: calcXmx "$@"
jpayne@69: 
jpayne@69: function reheader() {
jpayne@69: 	local CMD="java $EA $EOOM $z -cp $CP jgi.ReplaceHeaders $@"
jpayne@69: 	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: reheader "$@"