--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/fixgaps.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,83 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified September 11, 2019
+
+Description:  Uses paired read insert sizes to estimate the correct
+length of scaffold gaps, and resizes incorrectly-sized gaps.
+
+Usage:  fixgaps.sh in=mapped.sam ref=scaffolds.fa out=fixed.fa
+
+Standard parameters:
+in=<file>       Reads mapped to the reference; should be sam or bam.
+ref=<file>      Reference; may be fasta or fastq.
+out=<file>      Modified reference; may be fasta or fastq.
+overwrite=f     (ow) Set to false to force the program to abort rather than
+                overwrite an existing file.
+
+Processing parameters:
+gap=10          Consider any consecutive streak of Ns at least this long to
+                be a scaffold break.  Gaps will not be resized to less than
+                this.
+border=0.4      Ignore the outermost (border*readlen) of an insert (read pair)
+                when incrementing coverage.  A higher value is more accurate 
+                but requires more coverage and/or longer inserts.  Range: 0-1.
+mindepth=10     Minimum spanning read pairs to correct a gap.
+
+Java Parameters:
+-Xmx            This will set Java's memory usage, overriding autodetection.
+                -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will
+                specify 200 megs. The max is typically 85% of physical memory.
+-eoom           This flag will cause the process to exit if an out-of-memory
+                exception occurs.  Requires Java 8u92+.
+-da             Disable assertions.
+
+Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
+"
+}
+
+#This block allows symlinked shellscripts to correctly set classpath.
+pushd . > /dev/null
+DIR="${BASH_SOURCE[0]}"
+while [ -h "$DIR" ]; do
+  cd "$(dirname "$DIR")"
+  DIR="$(readlink "$(basename "$DIR")")"
+done
+cd "$(dirname "$DIR")"
+DIR="$(pwd)/"
+popd > /dev/null
+
+#DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
+CP="$DIR""current/"
+
+z="-Xmx4g"
+z2="-Xms4g"
+set=0
+
+if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
+	usage
+	exit
+fi
+
+calcXmx () {
+	source "$DIR""/calcmem.sh"
+	setEnvironment
+	parseXmx "$@"
+	if [[ $set == 1 ]]; then
+		return
+	fi
+	freeRam 4000m 84
+	z="-Xmx${RAM}m"
+	z2="-Xms${RAM}m"
+}
+calcXmx "$@"
+
+fixgaps() {
+	local CMD="java $EA $EOOM $z -cp $CP consensus.FixScaffoldGaps $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+fixgaps "$@"