Mercurial > repos > rliterman > csp2
annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/getreads.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 February 17, 2015 |
| jpayne@69 | 7 |
| jpayne@69 | 8 Description: Selects reads with designated numeric IDs. |
| jpayne@69 | 9 |
| jpayne@69 | 10 Usage: getreads.sh in=<file> id=<number,number,number...> out=<file> |
| jpayne@69 | 11 |
| jpayne@69 | 12 The first read (or pair) has ID 0, the second read (or pair) has ID 1, etc. |
| jpayne@69 | 13 |
| jpayne@69 | 14 Parameters: |
| jpayne@69 | 15 in=<file> Specify the input file, or stdin. |
| jpayne@69 | 16 out=<file> Specify the output file, or stdout. |
| jpayne@69 | 17 id= Comma delimited list of numbers or ranges, in any order. |
| jpayne@69 | 18 For example: id=5,93,17-31,8,0,12-13 |
| 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="-Xmx200m" |
| jpayne@69 | 39 set=0 |
| jpayne@69 | 40 |
| jpayne@69 | 41 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then |
| jpayne@69 | 42 usage |
| jpayne@69 | 43 exit |
| jpayne@69 | 44 fi |
| jpayne@69 | 45 |
| jpayne@69 | 46 calcXmx () { |
| jpayne@69 | 47 source "$DIR""/calcmem.sh" |
| jpayne@69 | 48 setEnvironment |
| jpayne@69 | 49 parseXmx "$@" |
| jpayne@69 | 50 } |
| jpayne@69 | 51 calcXmx "$@" |
| jpayne@69 | 52 |
| jpayne@69 | 53 function tf() { |
| jpayne@69 | 54 local CMD="java $EA $EOOM $z -cp $CP jgi.GetReads $@" |
| jpayne@69 | 55 echo $CMD >&2 |
| jpayne@69 | 56 eval $CMD |
| jpayne@69 | 57 } |
| jpayne@69 | 58 |
| jpayne@69 | 59 tf "$@" |