1#!/usr/local/bin/bash 2 3usage(){ 4echo " 5Written by Brian Bushnell 6Last modified September 11, 2019 7 8Description: Uses paired read insert sizes to estimate the correct 9length of scaffold gaps, and resizes incorrectly-sized gaps. 10 11Usage: fixgaps.sh in=mapped.sam ref=scaffolds.fa out=fixed.fa 12 13Standard parameters: 14in=<file> Reads mapped to the reference; should be sam or bam. 15ref=<file> Reference; may be fasta or fastq. 16out=<file> Modified reference; may be fasta or fastq. 17overwrite=f (ow) Set to false to force the program to abort rather than 18 overwrite an existing file. 19 20Processing parameters: 21gap=10 Consider any consecutive streak of Ns at least this long to 22 be a scaffold break. Gaps will not be resized to less than 23 this. 24border=0.4 Ignore the outermost (border*readlen) of an insert (read pair) 25 when incrementing coverage. A higher value is more accurate 26 but requires more coverage and/or longer inserts. Range: 0-1. 27mindepth=10 Minimum spanning read pairs to correct a gap. 28 29Java Parameters: 30-Xmx This will set Java's memory usage, overriding autodetection. 31 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will 32 specify 200 megs. The max is typically 85% of physical memory. 33-eoom This flag will cause the process to exit if an out-of-memory 34 exception occurs. Requires Java 8u92+. 35-da Disable assertions. 36 37Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 38" 39} 40 41#This block allows symlinked shellscripts to correctly set classpath. 42pushd . > /dev/null 43DIR="${BASH_SOURCE[0]}" 44while [ -h "$DIR" ]; do 45 cd "$(dirname "$DIR")" 46 DIR="$(readlink "$(basename "$DIR")")" 47done 48cd "$(dirname "$DIR")" 49DIR="$(pwd)/" 50popd > /dev/null 51 52#DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" 53CP="$DIR""current/" 54 55z="-Xmx4g" 56z2="-Xms4g" 57set=0 58 59if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then 60 usage 61 exit 62fi 63 64calcXmx () { 65 source "$DIR""/calcmem.sh" 66 setEnvironment 67 parseXmx "$@" 68 if [[ $set == 1 ]]; then 69 return 70 fi 71 freeRam 4000m 84 72 z="-Xmx${RAM}m" 73 z2="-Xms${RAM}m" 74} 75calcXmx "$@" 76 77fixgaps() { 78 local CMD="java $EA $EOOM $z -cp $CP consensus.FixScaffoldGaps $@" 79 echo $CMD >&2 80 eval $CMD 81} 82 83fixgaps "$@" 84