Mercurial > repos > rliterman > csp2
comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/summarizescafstats.sh @ 69:33d812a61356
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 17:55:14 -0400 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| 67:0e9998148a16 | 69:33d812a61356 |
|---|---|
| 1 #!/bin/bash | |
| 2 | |
| 3 usage(){ | |
| 4 echo " | |
| 5 Written by Brian Bushnell | |
| 6 Last modified May 26, 2015 | |
| 7 | |
| 8 Description: Summarizes the scafstats output of BBMap for evaluation | |
| 9 of cross-contamination. The intended use is to map multiple libraries or | |
| 10 assemblies, of different multiplexed organisms, to a concatenated reference | |
| 11 containing one fused scaffold per organism. This will convert all of the | |
| 12 resulting stats files (one per library) to a single text file, with multiple | |
| 13 columns, indicating how much of the input hit the primary versus nonprimary | |
| 14 scaffolds. | |
| 15 | |
| 16 Usage: summarizescafstats.sh in=<file,file...> out=<file> | |
| 17 | |
| 18 You can alternatively use a wildcard, like this: | |
| 19 summarizescafstats.sh scafstats_*.txt out=summary.txt | |
| 20 | |
| 21 Parameters: | |
| 22 in=<file> A list of stats files, or a text file containing one stats file name per line. | |
| 23 out=<file> Destination for summary. | |
| 24 | |
| 25 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. | |
| 26 " | |
| 27 } | |
| 28 | |
| 29 #This block allows symlinked shellscripts to correctly set classpath. | |
| 30 pushd . > /dev/null | |
| 31 DIR="${BASH_SOURCE[0]}" | |
| 32 while [ -h "$DIR" ]; do | |
| 33 cd "$(dirname "$DIR")" | |
| 34 DIR="$(readlink "$(basename "$DIR")")" | |
| 35 done | |
| 36 cd "$(dirname "$DIR")" | |
| 37 DIR="$(pwd)/" | |
| 38 popd > /dev/null | |
| 39 | |
| 40 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" | |
| 41 CP="$DIR""current/" | |
| 42 | |
| 43 z="-Xmx120m" | |
| 44 set=0 | |
| 45 | |
| 46 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then | |
| 47 usage | |
| 48 exit | |
| 49 fi | |
| 50 | |
| 51 calcXmx () { | |
| 52 source "$DIR""/calcmem.sh" | |
| 53 setEnvironment | |
| 54 parseXmx "$@" | |
| 55 } | |
| 56 calcXmx "$@" | |
| 57 | |
| 58 summarizescafstats() { | |
| 59 local CMD="java $EA $EOOM $z -cp $CP driver.SummarizeCoverage $@" | |
| 60 # echo $CMD >&2 | |
| 61 eval $CMD | |
| 62 } | |
| 63 | |
| 64 summarizescafstats "$@" |