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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/countgc.sh @ 69:33d812a61356

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 17:55:14 -0400
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67:0e9998148a16 69:33d812a61356
1 #!/bin/bash
2
3 usage(){
4 echo "
5 Written by Brian Bushnell
6 Last modified January 21, 2015
7
8 Description: Counts GC content of reads or scaffolds.
9
10 Usage: countgc in=<input> out=<output> format=<format>
11
12 Input may be stdin or a fasta or fastq file, compressed or uncompressed.
13 Output (which is optional) is tab-delimited.
14 format=1: name length A C G T N
15 format=2: name GC
16 format=4: name length GC
17 Note that in format 1, A+C+G+T=1 even when N is nonzero.
18
19 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
20 "
21 }
22
23 #This block allows symlinked shellscripts to correctly set classpath.
24 pushd . > /dev/null
25 DIR="${BASH_SOURCE[0]}"
26 while [ -h "$DIR" ]; do
27 cd "$(dirname "$DIR")"
28 DIR="$(readlink "$(basename "$DIR")")"
29 done
30 cd "$(dirname "$DIR")"
31 DIR="$(pwd)/"
32 popd > /dev/null
33
34 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
35 CP="$DIR""current/"
36
37 z="-Xmx120m"
38 set=0
39
40 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
41 usage
42 exit
43 fi
44
45 calcXmx () {
46 source "$DIR""/calcmem.sh"
47 setEnvironment
48 parseXmx "$@"
49 }
50 calcXmx "$@"
51
52 countgc() {
53 local CMD="java $EA $EOOM $z -cp $CP jgi.CountGC $@"
54 echo $CMD >&2
55 eval $CMD
56 }
57
58 countgc "$@"