1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
|
#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified December 19, 2018
Description: Generates a length histogram of input reads.
Usage: readlength.sh in=<input file>
in=<file> The 'in=' flag is needed only if the input file is not the first parameter. 'in=stdin.fq' will pipe from standard in.
in2=<file> Use this if 2nd read of pairs are in a different file.
out=<file> Write the histogram to this file. Default is stdout.
bin=10 Set the histogram bin size.
max=80000 Set the max read length to track.
round=f Places reads in the closest bin, rather than the highest bin of at least readlength.
nzo=t (nonzeroonly) Do not print empty bins.
reads=-1 If nonnegative, stop after this many reads.
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/"
z="-Xmx400m"
z2="-Xms400m"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
}
calcXmx "$@"
stats() {
local CMD="java $EA $EOOM $z -cp $CP jgi.MakeLengthHistogram $@"
# echo $CMD >&2
eval $CMD
}
stats "$@"
|
