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jpayne@69
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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 April 1, 2020
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7
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8 Description: Renames reads to <prefix>_<number> where you specify the prefix
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9 and the numbers are ordered. There are other renaming modes too.
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10 If reads are paired, pairs should be processed together; if reads are
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11 interleaved, the interleaved flag should be set. This ensures that if a
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12 read number (such as 1: or 2:) is added, it will be added correctly.
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13
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14 Usage: rename.sh in=<file> in2=<file2> out=<outfile> out2=<outfile2> prefix=<>
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15
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16 in2 and out2 are for paired reads and are optional.
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17 If input is paired and there is only one output file, it will be written interleaved.
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18
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19 Parameters:
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20 prefix= The string to prepend to existing read names.
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21 ow=f (overwrite) Overwrites files that already exist.
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22 zl=4 (ziplevel) Set compression level, 1 (low) to 9 (max).
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23 int=f (interleaved) Determines whether INPUT file is considered interleaved.
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24 fastawrap=70 Length of lines in fasta output.
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25 minscaf=1 Ignore fasta reads shorter than this.
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26 qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto.
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27 qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input).
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28 ignorebadquality=f (ibq) Fix out-of-range quality values instead of crashing with a warning.
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29
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30 Renaming modes (if not default):
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31 renamebyinsert=f Rename the read to indicate its correct insert size.
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32 renamebymapping=f Rename the read to indicate its correct mapping coordinates.
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33 renamebytrim=f Rename the read to indicate its correct post-trimming length.
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34 addprefix=f Rename the read by prepending the prefix to the existing name.
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35 prefixonly=f Only use the prefix; don't add _<number>
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36 addunderscore=t Add an underscore after the prefix (if there is a prefix).
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37 addpairnum=t Add a pairnum (e.g. ' 1:') to paired reads in some modes.
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38 fixsra=f Fixes headers of SRA reads renamed from Illumina.
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39 Specifically, it converts something like this:
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40 SRR17611.11 HWI-ST79:17:D091UACXX:4:1101:210:824 length=75
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41 ...into this:
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42 HWI-ST79:17:D091UACXX:4:1101:210:824 1:
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43
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44 Sampling parameters:
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45 reads=-1 Set to a positive number to only process this many INPUT reads (or pairs), then quit.
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46
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47 Java Parameters:
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48 -Xmx This will set Java's memory usage, overriding autodetection.
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49 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
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50 The max is typically 85% of physical memory.
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51 -eoom This flag will cause the process to exit if an
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52 out-of-memory exception occurs. Requires Java 8u92+.
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53 -da Disable assertions.
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54
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55 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
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56 "
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57 }
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58
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59 #This block allows symlinked shellscripts to correctly set classpath.
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60 pushd . > /dev/null
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61 DIR="${BASH_SOURCE[0]}"
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62 while [ -h "$DIR" ]; do
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63 cd "$(dirname "$DIR")"
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64 DIR="$(readlink "$(basename "$DIR")")"
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65 done
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66 cd "$(dirname "$DIR")"
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67 DIR="$(pwd)/"
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68 popd > /dev/null
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69
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70 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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71 CP="$DIR""current/"
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72
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73 z="-Xmx1g"
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74 set=0
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75
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76 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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77 usage
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78 exit
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79 fi
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80
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81 calcXmx () {
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82 source "$DIR""/calcmem.sh"
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83 setEnvironment
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84 parseXmx "$@"
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85 }
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86 calcXmx "$@"
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87
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88 function rename() {
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89 local CMD="java $EA $EOOM $z -cp $CP jgi.RenameReads $@"
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90 echo $CMD >&2
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91 eval $CMD
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92 }
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93
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94 rename "$@"
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