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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 May 23, 2016
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7
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8 Description: Replaces read names with names from another file.
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9 The other file can either be sequences or simply names, with
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10 one name per line (and no > or @ symbols). If you use one name
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11 per line, please give the file a .header extension.
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12
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13 Usage: replaceheaders.sh in=<file> hin=<headers file> out=<out file>
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14
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15 Parameters:
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16 in= Input sequences. Use in2 for a second paired file.
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17 in= Header input sequences. Use hin2 for a second paired file.
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18 out= Output sequences. Use out2 for a second paired file.
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19 ow=f (overwrite) Overwrites files that already exist.
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20 zl=4 (ziplevel) Set compression level, 1 (low) to 9 (max).
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21 int=f (interleaved) Determines whether INPUT file is considered interleaved.
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22 fastawrap=70 Length of lines in fasta output.
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23 qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto.
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24 qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input).
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25
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26 Renaming modes (if not default):
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27 addprefix=f Rename the read by prepending the new name to the existing name.
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28
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29 Sampling parameters:
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30 reads=-1 Set to a positive number to only process this many INPUT reads (or pairs), then quit.
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31
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32 Java Parameters:
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33 -Xmx This will set Java's memory usage, overriding autodetection.
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34 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
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35 The max is typically 85% of physical memory.
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36 -eoom This flag will cause the process to exit if an
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37 out-of-memory exception occurs. Requires Java 8u92+.
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38 -da Disable assertions.
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39
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40 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
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41 "
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42 }
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43
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44 #This block allows symlinked shellscripts to correctly set classpath.
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45 pushd . > /dev/null
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46 DIR="${BASH_SOURCE[0]}"
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47 while [ -h "$DIR" ]; do
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48 cd "$(dirname "$DIR")"
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49 DIR="$(readlink "$(basename "$DIR")")"
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50 done
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51 cd "$(dirname "$DIR")"
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52 DIR="$(pwd)/"
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53 popd > /dev/null
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54
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55 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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56 CP="$DIR""current/"
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57
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58 z="-Xmx1g"
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59 set=0
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60
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61 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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62 usage
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63 exit
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64 fi
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65
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66 calcXmx () {
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67 source "$DIR""/calcmem.sh"
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68 setEnvironment
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69 parseXmx "$@"
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70 }
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71 calcXmx "$@"
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72
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73 function reheader() {
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74 local CMD="java $EA $EOOM $z -cp $CP jgi.ReplaceHeaders $@"
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75 echo $CMD >&2
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76 eval $CMD
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77 }
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78
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79 reheader "$@"
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