Mercurial > repos > rliterman > csp2
annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/splitsam6way.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 June 15, 2017 |
| jpayne@69 | 7 |
| jpayne@69 | 8 Description: Splits sam reads into 6 output files depending on mapping. |
| jpayne@69 | 9 |
| jpayne@69 | 10 Usage: splitsam6way.sh <input> <r1plus> <r1minus> <r1unmapped> <r2plus> <r2minus> <r2unmapped> |
| jpayne@69 | 11 |
| jpayne@69 | 12 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. |
| jpayne@69 | 13 " |
| jpayne@69 | 14 } |
| jpayne@69 | 15 |
| jpayne@69 | 16 #This block allows symlinked shellscripts to correctly set classpath. |
| jpayne@69 | 17 pushd . > /dev/null |
| jpayne@69 | 18 DIR="${BASH_SOURCE[0]}" |
| jpayne@69 | 19 while [ -h "$DIR" ]; do |
| jpayne@69 | 20 cd "$(dirname "$DIR")" |
| jpayne@69 | 21 DIR="$(readlink "$(basename "$DIR")")" |
| jpayne@69 | 22 done |
| jpayne@69 | 23 cd "$(dirname "$DIR")" |
| jpayne@69 | 24 DIR="$(pwd)/" |
| jpayne@69 | 25 popd > /dev/null |
| jpayne@69 | 26 |
| jpayne@69 | 27 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" |
| jpayne@69 | 28 CP="$DIR""current/" |
| jpayne@69 | 29 set=0 |
| jpayne@69 | 30 |
| jpayne@69 | 31 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then |
| jpayne@69 | 32 usage |
| jpayne@69 | 33 exit |
| jpayne@69 | 34 fi |
| jpayne@69 | 35 |
| jpayne@69 | 36 calcXmx () { |
| jpayne@69 | 37 source "$DIR""/calcmem.sh" |
| jpayne@69 | 38 setEnvironment |
| jpayne@69 | 39 parseXmx "$@" |
| jpayne@69 | 40 } |
| jpayne@69 | 41 calcXmx "$@" |
| jpayne@69 | 42 |
| jpayne@69 | 43 function split() { |
| jpayne@69 | 44 local CMD="java $EA $EOOM -Xmx128m -Xms128m -cp $CP jgi.SplitSam6Way $@" |
| jpayne@69 | 45 echo $CMD >&2 |
| jpayne@69 | 46 eval $CMD |
| jpayne@69 | 47 } |
| jpayne@69 | 48 |
| jpayne@69 | 49 split "$@" |