|
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 November 9, 2016
|
|
jpayne@69
|
7
|
|
jpayne@69
|
8 Description: Re-pairs reads that became disordered or had some mates eliminated.
|
|
jpayne@69
|
9 Please read bbmap/docs/guides/RepairGuide.txt for more information.
|
|
jpayne@69
|
10
|
|
jpayne@69
|
11 Usage: repair.sh in=<input file> out=<pair output> outs=<singleton output>
|
|
jpayne@69
|
12
|
|
jpayne@69
|
13 Input may be fasta, fastq, or sam, compressed or uncompressed.
|
|
jpayne@69
|
14
|
|
jpayne@69
|
15 Parameters:
|
|
jpayne@69
|
16 in=<file> The 'in=' flag is needed if the input file is not the first
|
|
jpayne@69
|
17 parameter. 'in=stdin' will pipe from standard in.
|
|
jpayne@69
|
18 in2=<file> Use this if 2nd read of pairs are in a different file.
|
|
jpayne@69
|
19 out=<file> The 'out=' flag is needed if the output file is not the second
|
|
jpayne@69
|
20 parameter. 'out=stdout' will pipe to standard out.
|
|
jpayne@69
|
21 out2=<file> Use this to write 2nd read of pairs to a different file.
|
|
jpayne@69
|
22 outs=<file> (outsingle) Write singleton reads here.
|
|
jpayne@69
|
23 overwrite=t (ow) Set to false to force the program to abort rather than
|
|
jpayne@69
|
24 overwrite an existing file.
|
|
jpayne@69
|
25 showspeed=t (ss) Set to 'f' to suppress display of processing speed.
|
|
jpayne@69
|
26 ziplevel=2 (zl) Set to 1 (lowest) through 9 (max) to change compression
|
|
jpayne@69
|
27 level; lower compression is faster.
|
|
jpayne@69
|
28 fint=f (fixinterleaving) Fixes corrupted interleaved files using read
|
|
jpayne@69
|
29 names. Only use on files with broken interleaving - correctly
|
|
jpayne@69
|
30 interleaved files from which some reads were removed.
|
|
jpayne@69
|
31 repair=t (rp) Fixes arbitrarily corrupted paired reads by using read
|
|
jpayne@69
|
32 names. Uses much more memory than 'fint' mode.
|
|
jpayne@69
|
33 ain=f (allowidenticalnames) When detecting pair names, allows
|
|
jpayne@69
|
34 identical names, instead of requiring /1 and /2 or 1: and 2:
|
|
jpayne@69
|
35
|
|
jpayne@69
|
36 Java Parameters:
|
|
jpayne@69
|
37 -Xmx This will set Java's memory usage, overriding autodetection.
|
|
jpayne@69
|
38 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will
|
|
jpayne@69
|
39 specify 200 megs. The max is typically 85% of physical memory.
|
|
jpayne@69
|
40 -eoom This flag will cause the process to exit if an out-of-memory
|
|
jpayne@69
|
41 exception occurs. Requires Java 8u92+.
|
|
jpayne@69
|
42 -da Disable assertions.
|
|
jpayne@69
|
43
|
|
jpayne@69
|
44 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
|
|
jpayne@69
|
45 "
|
|
jpayne@69
|
46 }
|
|
jpayne@69
|
47
|
|
jpayne@69
|
48 #This block allows symlinked shellscripts to correctly set classpath.
|
|
jpayne@69
|
49 pushd . > /dev/null
|
|
jpayne@69
|
50 DIR="${BASH_SOURCE[0]}"
|
|
jpayne@69
|
51 while [ -h "$DIR" ]; do
|
|
jpayne@69
|
52 cd "$(dirname "$DIR")"
|
|
jpayne@69
|
53 DIR="$(readlink "$(basename "$DIR")")"
|
|
jpayne@69
|
54 done
|
|
jpayne@69
|
55 cd "$(dirname "$DIR")"
|
|
jpayne@69
|
56 DIR="$(pwd)/"
|
|
jpayne@69
|
57 popd > /dev/null
|
|
jpayne@69
|
58
|
|
jpayne@69
|
59 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
|
|
jpayne@69
|
60 CP="$DIR""current/"
|
|
jpayne@69
|
61
|
|
jpayne@69
|
62 z="-Xmx4g"
|
|
jpayne@69
|
63 z2="-Xms4g"
|
|
jpayne@69
|
64 set=0
|
|
jpayne@69
|
65
|
|
jpayne@69
|
66 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
|
|
jpayne@69
|
67 usage
|
|
jpayne@69
|
68 exit
|
|
jpayne@69
|
69 fi
|
|
jpayne@69
|
70
|
|
jpayne@69
|
71 calcXmx () {
|
|
jpayne@69
|
72 source "$DIR""/calcmem.sh"
|
|
jpayne@69
|
73 setEnvironment
|
|
jpayne@69
|
74 parseXmx "$@"
|
|
jpayne@69
|
75 if [[ $set == 1 ]]; then
|
|
jpayne@69
|
76 return
|
|
jpayne@69
|
77 fi
|
|
jpayne@69
|
78 freeRam 4000m 84
|
|
jpayne@69
|
79 z="-Xmx${RAM}m"
|
|
jpayne@69
|
80 z2="-Xms${RAM}m"
|
|
jpayne@69
|
81 }
|
|
jpayne@69
|
82 calcXmx "$@"
|
|
jpayne@69
|
83
|
|
jpayne@69
|
84 repair() {
|
|
jpayne@69
|
85 local CMD="java $EA $EOOM $z -cp $CP jgi.SplitPairsAndSingles rp $@"
|
|
jpayne@69
|
86 echo $CMD >&2
|
|
jpayne@69
|
87 eval $CMD
|
|
jpayne@69
|
88 }
|
|
jpayne@69
|
89
|
|
jpayne@69
|
90 repair "$@"
|
