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1 #!/bin/bash
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2
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3 usage(){
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4 echo "
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5 Written by Brian Bushnell
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6 Last modified March 21, 2018
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7
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8 Description: Converts sam/bam to fastq rapidly with multiple threads.
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9 bam files require samtools or sambamba in the path.
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10
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11 Usage: streamsam.sh in=<file> out=<file>
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12
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13 Filtering parameters:
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14 minpos= Ignore alignments not overlapping this range.
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15 maxpos= Ignore alignments not overlapping this range.
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16 minmapq= Ignore alignments with mapq below this.
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17 maxmapq= Ignore alignments with mapq above this.
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18 contigs= Comma-delimited list of contig names to include. These
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19 should have no spaces, or underscores instead of spaces.
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20 mapped=t Include mapped reads.
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21 unmapped=t Include unmapped reads.
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22 secondary=f Include secondary alignments.
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23 supplimentary=t Include supplimentary alignments.
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24 lengthzero=f Include alignments without bases.
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25 invert=f Invert sam filters.
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26 ordered=t Keep reads in input order. False is faster.
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27 ref=<file> Optional reference file.
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28
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29 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
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30 "
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31 }
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32
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33 #This block allows symlinked shellscripts to correctly set classpath.
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34 pushd . > /dev/null
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35 DIR="${BASH_SOURCE[0]}"
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36 while [ -h "$DIR" ]; do
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37 cd "$(dirname "$DIR")"
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38 DIR="$(readlink "$(basename "$DIR")")"
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39 done
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40 cd "$(dirname "$DIR")"
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41 DIR="$(pwd)/"
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42 popd > /dev/null
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43
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44 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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45 CP="$DIR""current/"
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46
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47 z="-Xmx1g"
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48 set=0
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49
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50 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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51 usage
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52 exit
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53 fi
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54
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55 calcXmx () {
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56 source "$DIR""/calcmem.sh"
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57 setEnvironment
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58 parseXmx "$@"
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59 }
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60 calcXmx "$@"
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61
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62 streamsam() {
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63 local CMD="java $EA $EOOM $z -cp $CP stream.SamStreamerWrapper $@"
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64 echo $CMD >&2
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65 eval $CMD
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66 }
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67
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68 streamsam "$@"
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