--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/bbmapskimmer.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,54 @@
+#!/bin/bash
+
+#This is a version of BBMap designed to final all sites above a given threshold,
+#rather than the single best site.  Syntax is the same as BBMap.
+
+usage(){
+	bash "$DIR"bbmap.sh
+}
+
+#This block allows symlinked shellscripts to correctly set classpath.
+pushd . > /dev/null
+DIR="${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="$DIR""current/"
+JNI="-Djava.library.path=""$DIR""jni/"
+JNI=""
+
+z="-Xmx1g"
+z2="-Xms1g"
+set=0
+
+if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
+	usage
+	exit
+fi
+
+calcXmx () {
+	source "$DIR""/calcmem.sh"
+	setEnvironment
+	parseXmx "$@"
+	if [[ $set == 1 ]]; then
+		return
+	fi
+	freeRam 3200m 84
+	z="-Xmx${RAM}m"
+	z2="-Xms${RAM}m"
+}
+calcXmx "$@"
+
+mapPacBioSkimmer() {
+	local CMD="java $EA $EOOM $z $z2 $JNI -cp $CP align2.BBMapPacBioSkimmer build=1 overwrite=true minratio=0.40 fastareadlen=6000 ambig=all minscaf=100 startpad=10000 stoppad=10000 midpad=6000 $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+mapPacBioSkimmer "$@"