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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 August 9, 2018
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7
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8 Description: Generates statistics about flowcell positions.
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9
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10 Usage: plotflowcell.sh in=<input> out=<output>
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11
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12 Input parameters:
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13 in=<file> Primary input file.
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14 in2=<file> Second input file for paired reads in two files.
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15 indump=<file> Specify an already-made dump file to use instead of
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16 analyzing the input reads.
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17 reads=-1 Process this number of reads, then quit (-1 means all).
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18 interleaved=auto Set true/false to override autodetection of the
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19 input file as paired interleaved.
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20
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21 Output parameters:
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22 out=<file> Output file for filtered reads.
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23 dump=<file> Write a summary of quality information by coordinates.
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24
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25 Tile parameters:
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26 xsize=500 Initial width of micro-tiles.
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27 ysize=500 Initial height of micro-tiles.
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28 size= Allows setting xsize and ysize tot he same value.
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29 target=800 Iteratively increase the size of micro-tiles until they
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30 contain an average of at least this number of reads.
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31
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32 Other parameters:
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33 trimq=-1 If set to a positive number, trim reads to that quality
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34 level instead of filtering them.
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35 qtrim=r If trimq is positive, to quality trimming on this end
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36 of the reads. Values are r, l, and rl for right,
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37 left, and both ends.
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38
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39 Java Parameters:
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40 -Xmx This will set Java's memory usage, overriding autodetection.
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41 -Xmx20g will specify 20 GB of RAM; -Xmx200m will specify
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42 200 MB. The max is typically 85% of physical memory.
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43 -eoom This flag will cause the process to exit if an
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44 out-of-memory exception occurs. Requires Java 8u92+.
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45 -da Disable assertions.
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46
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47 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
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48 "
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49 }
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50
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51 #This block allows symlinked shellscripts to correctly set classpath.
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52 pushd . > /dev/null
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53 DIR="${BASH_SOURCE[0]}"
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54 while [ -h "$DIR" ]; do
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55 cd "$(dirname "$DIR")"
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56 DIR="$(readlink "$(basename "$DIR")")"
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57 done
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58 cd "$(dirname "$DIR")"
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59 DIR="$(pwd)/"
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60 popd > /dev/null
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61
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62 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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63 CP="$DIR""current/"
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64
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65 z="-Xmx8g"
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66 z2="-Xms8g"
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67 set=0
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68
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69 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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70 usage
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71 exit
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72 fi
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73
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74 calcXmx () {
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75 source "$DIR""/calcmem.sh"
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76 setEnvironment
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77 parseXmx "$@"
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78 if [[ $set == 1 ]]; then
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79 return
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80 fi
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81 freeRam 3200m 84
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82 z="-Xmx${RAM}m"
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83 z2="-Xms${RAM}m"
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84 }
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85 calcXmx "$@"
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86
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87 plotflowcell() {
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88 local CMD="java $EA $EOOM $z $z2 -cp $CP hiseq.PlotFlowCell $@"
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89 echo $CMD >&2
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90 eval $CMD
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91 }
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92
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93 plotflowcell "$@"
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