jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Brian Bushnell
jpayne@69: Last modified November 9, 2016
jpayne@69: 
jpayne@69: Description:  Re-pairs reads that became disordered or had some mates eliminated.
jpayne@69: Please read bbmap/docs/guides/RepairGuide.txt for more information.
jpayne@69: 
jpayne@69: Usage:  repair.sh in=<input file> out=<pair output> outs=<singleton output>
jpayne@69: 
jpayne@69: Input may be fasta, fastq, or sam, compressed or uncompressed.
jpayne@69: 
jpayne@69: Parameters:
jpayne@69: in=<file>       The 'in=' flag is needed if the input file is not the first 
jpayne@69:                 parameter.  'in=stdin' will pipe from standard in.
jpayne@69: in2=<file>      Use this if 2nd read of pairs are in a different file.
jpayne@69: out=<file>      The 'out=' flag is needed if the output file is not the second
jpayne@69:                 parameter.  'out=stdout' will pipe to standard out.
jpayne@69: out2=<file>     Use this to write 2nd read of pairs to a different file.
jpayne@69: outs=<file>     (outsingle) Write singleton reads here.
jpayne@69: overwrite=t     (ow) Set to false to force the program to abort rather than
jpayne@69:                 overwrite an existing file.
jpayne@69: showspeed=t     (ss) Set to 'f' to suppress display of processing speed.
jpayne@69: ziplevel=2      (zl) Set to 1 (lowest) through 9 (max) to change compression
jpayne@69:                 level; lower compression is faster.
jpayne@69: fint=f          (fixinterleaving) Fixes corrupted interleaved files using read
jpayne@69:                 names.  Only use on files with broken interleaving - correctly
jpayne@69:                 interleaved files from which some reads were removed.
jpayne@69: repair=t        (rp) Fixes arbitrarily corrupted paired reads by using read 
jpayne@69:                 names.  Uses much more memory than 'fint' mode.
jpayne@69: ain=f           (allowidenticalnames) When detecting pair names, allows 
jpayne@69:                 identical names, instead of requiring /1 and /2 or 1: and 2:
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
jpayne@69:                 specify 200 megs. The max is typically 85% of physical memory.
jpayne@69: -eoom           This flag will cause the process to exit if an out-of-memory
jpayne@69:                 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="-Xmx4g"
jpayne@69: z2="-Xms4g"
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: 	if [[ $set == 1 ]]; then
jpayne@69: 		return
jpayne@69: 	fi
jpayne@69: 	freeRam 4000m 84
jpayne@69: 	z="-Xmx${RAM}m"
jpayne@69: 	z2="-Xms${RAM}m"
jpayne@69: }
jpayne@69: calcXmx "$@"
jpayne@69: 
jpayne@69: repair() {
jpayne@69: 	local CMD="java $EA $EOOM $z -cp $CP jgi.SplitPairsAndSingles rp $@"
jpayne@69: 	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: repair "$@"