--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/gradesam.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,52 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified May 23, 2014
+
+Description:  Grades mapping correctness of a sam file of synthetic reads with headers generated by RandomReads3.java
+
+Usage:   gradesam.sh in=<sam file> reads=<number of reads>
+
+Parameters:
+in=<file>       Specify the input sam file, or stdin.
+reads=<int>     Number of reads in mapper's input (i.e., the fastq file).
+thresh=20       Max deviation from correct location to be considered 'loosely correct'.
+blasr=f         Set to 't' for BLASR output; fixes extra information added to read names.
+ssaha2=f        Set to 't' for SSAHA2 or SMALT output; fixes incorrect soft-clipped read locations.
+quality=3       Reads with a mapping quality of this or below will be considered ambiguously mapped.
+bitset=t        Track read ID's to detect secondary alignments.
+                Necessary for mappers that incorrectly output multiple primary alignments per read.
+
+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/"
+set=0
+
+if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
+	usage
+	exit
+fi
+
+function gradesam() {
+	local CMD="java $EA $EOOM -Xmx200m -cp $CP align2.GradeSamFile $@"
+#	echo $CMD >&2
+	eval $CMD
+}
+
+gradesam "$@"