Mercurial > repos > rliterman > csp2
comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/consect.sh @ 69:33d812a61356
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 17:55:14 -0400 |
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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 October 25, 2016 | |
| 7 | |
| 8 Description: Generates the conservative consensus of multiple | |
| 9 error-correction tools. Corrections will be accepted only | |
| 10 if all tools agree. This tool is designed for substitutions only, | |
| 11 not indel corrections. | |
| 12 | |
| 13 Usage: consect.sh in=<file,file,file,...> out=<file> | |
| 14 | |
| 15 Standard parameters: | |
| 16 in= A comma-delimited list of files; minimum of 3. | |
| 17 All files must have reads in the same order. | |
| 18 The first file must contain the uncorrected reads. | |
| 19 All additional files must contain corrected reads. | |
| 20 out=<file> Output of consensus reads. | |
| 21 overwrite=f (ow) Set to false to force the program to abort rather than | |
| 22 overwrite an existing file. | |
| 23 | |
| 24 Processing parameters: | |
| 25 None yet! | |
| 26 | |
| 27 Java Parameters: | |
| 28 -Xmx This will set Java's memory usage, overriding autodetection. | |
| 29 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. | |
| 30 The max is typically 85% of physical memory. | |
| 31 -eoom This flag will cause the process to exit if an out-of-memory | |
| 32 exception occurs. Requires Java 8u92+. | |
| 33 -da Disable assertions. | |
| 34 | |
| 35 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. | |
| 36 " | |
| 37 } | |
| 38 | |
| 39 #This block allows symlinked shellscripts to correctly set classpath. | |
| 40 pushd . > /dev/null | |
| 41 DIR="${BASH_SOURCE[0]}" | |
| 42 while [ -h "$DIR" ]; do | |
| 43 cd "$(dirname "$DIR")" | |
| 44 DIR="$(readlink "$(basename "$DIR")")" | |
| 45 done | |
| 46 cd "$(dirname "$DIR")" | |
| 47 DIR="$(pwd)/" | |
| 48 popd > /dev/null | |
| 49 | |
| 50 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" | |
| 51 CP="$DIR""current/" | |
| 52 | |
| 53 z="-Xmx2g" | |
| 54 set=0 | |
| 55 | |
| 56 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then | |
| 57 usage | |
| 58 exit | |
| 59 fi | |
| 60 | |
| 61 calcXmx () { | |
| 62 source "$DIR""/calcmem.sh" | |
| 63 setEnvironment | |
| 64 parseXmx "$@" | |
| 65 } | |
| 66 calcXmx "$@" | |
| 67 | |
| 68 consect() { | |
| 69 local CMD="java $EA $EOOM $z -cp $CP jgi.Consect $@" | |
| 70 echo $CMD >&2 | |
| 71 eval $CMD | |
| 72 } | |
| 73 | |
| 74 consect "$@" |