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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/getreads.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 February 17, 2015
7
8 Description: Selects reads with designated numeric IDs.
9
10 Usage: getreads.sh in=<file> id=<number,number,number...> out=<file>
11
12 The first read (or pair) has ID 0, the second read (or pair) has ID 1, etc.
13
14 Parameters:
15 in=<file> Specify the input file, or stdin.
16 out=<file> Specify the output file, or stdout.
17 id= Comma delimited list of numbers or ranges, in any order.
18 For example: id=5,93,17-31,8,0,12-13
19
20 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
21 "
22 }
23
24 #This block allows symlinked shellscripts to correctly set classpath.
25 pushd . > /dev/null
26 DIR="${BASH_SOURCE[0]}"
27 while [ -h "$DIR" ]; do
28 cd "$(dirname "$DIR")"
29 DIR="$(readlink "$(basename "$DIR")")"
30 done
31 cd "$(dirname "$DIR")"
32 DIR="$(pwd)/"
33 popd > /dev/null
34
35 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
36 CP="$DIR""current/"
37
38 z="-Xmx200m"
39 set=0
40
41 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
42 usage
43 exit
44 fi
45
46 calcXmx () {
47 source "$DIR""/calcmem.sh"
48 setEnvironment
49 parseXmx "$@"
50 }
51 calcXmx "$@"
52
53 function tf() {
54 local CMD="java $EA $EOOM $z -cp $CP jgi.GetReads $@"
55 echo $CMD >&2
56 eval $CMD
57 }
58
59 tf "$@"