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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/bbest.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 November 4, 2015
7
8 Description: Calculates EST (expressed sequence tags) capture by an assembly from a sam file.
9 Designed to use BBMap output generated with these flags: k=13 maxindel=100000 customtag ordered
10
11 Usage: bbest.sh in=<sam file> out=<stats file>
12
13 Parameters:
14 in=<file> Specify a sam file (or stdin) containing mapped ests.
15 out=<file> Specify the output stats file (default is stdout).
16 ref=<file> Specify the reference file (optional).
17 est=<file> Specify the est fasta file (optional).
18 fraction=0.98 Min fraction of bases mapped to ref to be
19 considered 'all mapped'.
20
21 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
22 "
23 }
24
25 #This block allows symlinked shellscripts to correctly set classpath.
26 pushd . > /dev/null
27 DIR="${BASH_SOURCE[0]}"
28 while [ -h "$DIR" ]; do
29 cd "$(dirname "$DIR")"
30 DIR="$(readlink "$(basename "$DIR")")"
31 done
32 cd "$(dirname "$DIR")"
33 DIR="$(pwd)/"
34 popd > /dev/null
35
36 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
37 CP="$DIR""current/"
38
39 z="-Xmx120m"
40 z2="-Xms120m"
41 set=0
42
43 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
44 usage
45 exit
46 fi
47
48 calcXmx () {
49 source "$DIR""/calcmem.sh"
50 setEnvironment
51 parseXmx "$@"
52 }
53 calcXmx "$@"
54
55 function bbest() {
56 local CMD="java $EA $EOOM $z -cp $CP jgi.SamToEst $@"
57 # echo $CMD >&2
58 eval $CMD
59 }
60
61 bbest "$@"