Mercurial > repos > rliterman > csp2
comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/summarizecoverage.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 April 5, 2020 | |
| 7 | |
| 8 Description: Summarizes coverage information from basecov files | |
| 9 created by pileup.sh. They should be named like | |
| 10 'sample1_basecov.txt' but other naming styles are fine too. | |
| 11 | |
| 12 Usage: summarizecoverage.sh *basecov.txt out=<output file> | |
| 13 | |
| 14 Parameters: | |
| 15 in=<file> 'in=' is not necessary. Any filename used as a | |
| 16 parameter will be assumed to be an input basecov file. | |
| 17 out=<file> Write the summary here. Default is stdout. | |
| 18 reflen=-1 If positive, use this as the total reference length. | |
| 19 Otherwise, assume basecov files report every ref base. | |
| 20 | |
| 21 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. | |
| 22 " | |
| 23 } | |
| 24 | |
| 25 #This block allows symlinked shellscripts to correctly set classpath. | |
| 26 pushd . > /dev/null | |
| 27 DIR="${BASH_SOURCE[0]}" | |
| 28 while [ -h "$DIR" ]; do | |
| 29 cd "$(dirname "$DIR")" | |
| 30 DIR="$(readlink "$(basename "$DIR")")" | |
| 31 done | |
| 32 cd "$(dirname "$DIR")" | |
| 33 DIR="$(pwd)/" | |
| 34 popd > /dev/null | |
| 35 | |
| 36 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" | |
| 37 CP="$DIR""current/" | |
| 38 | |
| 39 z="-Xmx200m" | |
| 40 set=0 | |
| 41 | |
| 42 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then | |
| 43 usage | |
| 44 exit | |
| 45 fi | |
| 46 | |
| 47 calcXmx () { | |
| 48 source "$DIR""/calcmem.sh" | |
| 49 setEnvironment | |
| 50 parseXmx "$@" | |
| 51 } | |
| 52 calcXmx "$@" | |
| 53 | |
| 54 summarize() { | |
| 55 local CMD="java $EA $EOOM $z -cp $CP covid.SummarizeCoverage $@" | |
| 56 # echo $CMD >&2 | |
| 57 eval $CMD | |
| 58 } | |
| 59 | |
| 60 summarize "$@" |