Mercurial > repos > rliterman > csp2
annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/readlength.sh @ 69:33d812a61356
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 17:55:14 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| jpayne@69 | 1 #!/bin/bash |
| jpayne@69 | 2 |
| jpayne@69 | 3 usage(){ |
| jpayne@69 | 4 echo " |
| jpayne@69 | 5 Written by Brian Bushnell |
| jpayne@69 | 6 Last modified December 19, 2018 |
| jpayne@69 | 7 Description: Generates a length histogram of input reads. |
| jpayne@69 | 8 |
| jpayne@69 | 9 Usage: readlength.sh in=<input file> |
| jpayne@69 | 10 |
| jpayne@69 | 11 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. |
| jpayne@69 | 12 in2=<file> Use this if 2nd read of pairs are in a different file. |
| jpayne@69 | 13 out=<file> Write the histogram to this file. Default is stdout. |
| jpayne@69 | 14 bin=10 Set the histogram bin size. |
| jpayne@69 | 15 max=80000 Set the max read length to track. |
| jpayne@69 | 16 round=f Places reads in the closest bin, rather than the highest bin of at least readlength. |
| jpayne@69 | 17 nzo=t (nonzeroonly) Do not print empty bins. |
| jpayne@69 | 18 reads=-1 If nonnegative, stop after this many reads. |
| jpayne@69 | 19 |
| jpayne@69 | 20 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. |
| jpayne@69 | 21 " |
| jpayne@69 | 22 } |
| jpayne@69 | 23 |
| jpayne@69 | 24 #This block allows symlinked shellscripts to correctly set classpath. |
| jpayne@69 | 25 pushd . > /dev/null |
| jpayne@69 | 26 DIR="${BASH_SOURCE[0]}" |
| jpayne@69 | 27 while [ -h "$DIR" ]; do |
| jpayne@69 | 28 cd "$(dirname "$DIR")" |
| jpayne@69 | 29 DIR="$(readlink "$(basename "$DIR")")" |
| jpayne@69 | 30 done |
| jpayne@69 | 31 cd "$(dirname "$DIR")" |
| jpayne@69 | 32 DIR="$(pwd)/" |
| jpayne@69 | 33 popd > /dev/null |
| jpayne@69 | 34 |
| jpayne@69 | 35 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" |
| jpayne@69 | 36 CP="$DIR""current/" |
| jpayne@69 | 37 |
| jpayne@69 | 38 z="-Xmx400m" |
| jpayne@69 | 39 z2="-Xms400m" |
| jpayne@69 | 40 set=0 |
| jpayne@69 | 41 |
| jpayne@69 | 42 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then |
| jpayne@69 | 43 usage |
| jpayne@69 | 44 exit |
| jpayne@69 | 45 fi |
| jpayne@69 | 46 |
| jpayne@69 | 47 calcXmx () { |
| jpayne@69 | 48 source "$DIR""/calcmem.sh" |
| jpayne@69 | 49 setEnvironment |
| jpayne@69 | 50 parseXmx "$@" |
| jpayne@69 | 51 } |
| jpayne@69 | 52 calcXmx "$@" |
| jpayne@69 | 53 |
| jpayne@69 | 54 stats() { |
| jpayne@69 | 55 local CMD="java $EA $EOOM $z -cp $CP jgi.MakeLengthHistogram $@" |
| jpayne@69 | 56 # echo $CMD >&2 |
| jpayne@69 | 57 eval $CMD |
| jpayne@69 | 58 } |
| jpayne@69 | 59 |
| jpayne@69 | 60 stats "$@" |