Mercurial > repos > rliterman > csp2
comparison 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 |
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| 67:0e9998148a16 | 69:33d812a61356 |
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| 1 #!/bin/bash | |
| 2 | |
| 3 usage(){ | |
| 4 echo " | |
| 5 Written by Brian Bushnell | |
| 6 Last modified June 15, 2017 | |
| 7 | |
| 8 Description: Splits sam reads into 6 output files depending on mapping. | |
| 9 | |
| 10 Usage: splitsam6way.sh <input> <r1plus> <r1minus> <r1unmapped> <r2plus> <r2minus> <r2unmapped> | |
| 11 | |
| 12 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. | |
| 13 " | |
| 14 } | |
| 15 | |
| 16 #This block allows symlinked shellscripts to correctly set classpath. | |
| 17 pushd . > /dev/null | |
| 18 DIR="${BASH_SOURCE[0]}" | |
| 19 while [ -h "$DIR" ]; do | |
| 20 cd "$(dirname "$DIR")" | |
| 21 DIR="$(readlink "$(basename "$DIR")")" | |
| 22 done | |
| 23 cd "$(dirname "$DIR")" | |
| 24 DIR="$(pwd)/" | |
| 25 popd > /dev/null | |
| 26 | |
| 27 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" | |
| 28 CP="$DIR""current/" | |
| 29 set=0 | |
| 30 | |
| 31 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then | |
| 32 usage | |
| 33 exit | |
| 34 fi | |
| 35 | |
| 36 calcXmx () { | |
| 37 source "$DIR""/calcmem.sh" | |
| 38 setEnvironment | |
| 39 parseXmx "$@" | |
| 40 } | |
| 41 calcXmx "$@" | |
| 42 | |
| 43 function split() { | |
| 44 local CMD="java $EA $EOOM -Xmx128m -Xms128m -cp $CP jgi.SplitSam6Way $@" | |
| 45 echo $CMD >&2 | |
| 46 eval $CMD | |
| 47 } | |
| 48 | |
| 49 split "$@" |