Mercurial > repos > rliterman > csp2

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 17:55:14 -0400
parents
children
comparison
equal deleted inserted replaced
67:0e9998148a16 69:33d812a61356
1 #!/bin/bash
2
3 usage(){
4 echo "
5 Written by Brian Bushnell
6 Last modified January 25, 2018
7
8 Description: Summarizes the output of BBSketch.
9
10 Usage: summarizesketch.sh in=<file,file...> out=<file>
11
12 You can alternately run 'summarizesketch.sh *.txt out=out.txt'
13
14 Parameters:
15 in=<file> A list of stats files, or a text file containing one stats file name per line.
16 out=<file> Destination for summary.
17 tree= A TaxTree file.
18 level=genus Ignore contaminants with the same taxonomy as the primary hit at this level.
19 unique=f Use the contaminant with the most unique hits rather than highest score.
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="-Xmx2g"
40 set=0
41
42 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
43 usage
44 exit
45 fi
46
47 calcXmx () {
48 source "$DIR""/calcmem.sh"
49 setEnvironment
50 parseXmx "$@"
51 }
52 calcXmx "$@"
53
54 summarizesketch() {
55 local CMD="java $EA $EOOM $z -cp $CP sketch.SummarizeSketchStats $@"
56 # echo $CMD >&2
57 eval $CMD
58 }
59
60 summarizesketch "$@"