Mercurial > repos > rliterman > csp2
annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/gradesam.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 May 23, 2014 |
| jpayne@69 | 7 |
| jpayne@69 | 8 Description: Grades mapping correctness of a sam file of synthetic reads with headers generated by RandomReads3.java |
| jpayne@69 | 9 |
| jpayne@69 | 10 Usage: gradesam.sh in=<sam file> reads=<number of reads> |
| jpayne@69 | 11 |
| jpayne@69 | 12 Parameters: |
| jpayne@69 | 13 in=<file> Specify the input sam file, or stdin. |
| jpayne@69 | 14 reads=<int> Number of reads in mapper's input (i.e., the fastq file). |
| jpayne@69 | 15 thresh=20 Max deviation from correct location to be considered 'loosely correct'. |
| jpayne@69 | 16 blasr=f Set to 't' for BLASR output; fixes extra information added to read names. |
| jpayne@69 | 17 ssaha2=f Set to 't' for SSAHA2 or SMALT output; fixes incorrect soft-clipped read locations. |
| jpayne@69 | 18 quality=3 Reads with a mapping quality of this or below will be considered ambiguously mapped. |
| jpayne@69 | 19 bitset=t Track read ID's to detect secondary alignments. |
| jpayne@69 | 20 Necessary for mappers that incorrectly output multiple primary alignments per read. |
| jpayne@69 | 21 |
| jpayne@69 | 22 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. |
| jpayne@69 | 23 " |
| jpayne@69 | 24 } |
| jpayne@69 | 25 |
| jpayne@69 | 26 #This block allows symlinked shellscripts to correctly set classpath. |
| jpayne@69 | 27 pushd . > /dev/null |
| jpayne@69 | 28 DIR="${BASH_SOURCE[0]}" |
| jpayne@69 | 29 while [ -h "$DIR" ]; do |
| jpayne@69 | 30 cd "$(dirname "$DIR")" |
| jpayne@69 | 31 DIR="$(readlink "$(basename "$DIR")")" |
| jpayne@69 | 32 done |
| jpayne@69 | 33 cd "$(dirname "$DIR")" |
| jpayne@69 | 34 DIR="$(pwd)/" |
| jpayne@69 | 35 popd > /dev/null |
| jpayne@69 | 36 |
| jpayne@69 | 37 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" |
| jpayne@69 | 38 CP="$DIR""current/" |
| jpayne@69 | 39 set=0 |
| jpayne@69 | 40 |
| jpayne@69 | 41 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then |
| jpayne@69 | 42 usage |
| jpayne@69 | 43 exit |
| jpayne@69 | 44 fi |
| jpayne@69 | 45 |
| jpayne@69 | 46 function gradesam() { |
| jpayne@69 | 47 local CMD="java $EA $EOOM -Xmx200m -cp $CP align2.GradeSamFile $@" |
| jpayne@69 | 48 # echo $CMD >&2 |
| jpayne@69 | 49 eval $CMD |
| jpayne@69 | 50 } |
| jpayne@69 | 51 |
| jpayne@69 | 52 gradesam "$@" |