1#!/usr/local/bin/bash
2
3usage(){
4echo "
5Written by Brian Bushnell
6Last modified September 1, 2016
7
8Description:  Filters reads by name.
9
10Usage:  filterbyname.sh in=<file> in2=<file2> out=<outfile> out2=<outfile2> names=<string,string,string> include=<t/f>
11
12in2 and out2 are for paired reads and are optional.
13If input is paired and there is only one output file, it will be written interleaved.
14Important!  Leading > and @ symbols are NOT part of sequence names;  they are part of
15the fasta, fastq, and sam specifications.  Therefore, this is correct:
16names=e.coli_K12
17And these are incorrect:
18names=>e.coli_K12
19names=@e.coli_K12
20
21Parameters:
22include=f       Set to 'true' to include the filtered names rather than excluding them.
23substring=f     Allow one name to be a substring of the other, rather than a full match.
24                   f: No substring matching.
25                   t: Bidirectional substring matching.
26                   header: Allow input read headers to be substrings of names in list.
27                   name: Allow names in list to be substrings of input read headers.
28prefix=f        Allow names to match read header prefixes.
29case=t          (casesensitive) Match case also.
30ow=t            (overwrite) Overwrites files that already exist.
31app=f           (append) Append to files that already exist.
32zl=4            (ziplevel) Set compression level, 1 (low) to 9 (max).
33int=f           (interleaved) Determines whether INPUT file is considered interleaved.
34names=          A list of strings or files.  The files can have one name per line, or
35                be a standard read file (fasta, fastq, or sam).
36minlen=0        Do not output reads shorter than this.
37ths=f           (truncateheadersymbol) Ignore a leading @ or > symbol in the names file.
38tws=f           (truncatewhitespace) Ignore leading or trailing whitespace in the names file.
39truncate=f      Set both ths and tws at the same time.
40
41Positional parameters:
42These optionally allow you to output only a portion of a sequence.  Zero-based, inclusive.
43Intended for a single sequence and include=t mode.
44from=-1         Only print bases starting at this position.
45to=-1           Only print bases up to this position.
46range=          Set from and to with a single flag.
47
48
49Java Parameters:
50-Xmx            This will set Java's memory usage, overriding autodetection.
51                -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
52                    The max is typically 85% of physical memory.
53-eoom           This flag will cause the process to exit if an out-of-memory
54                exception occurs.  Requires Java 8u92+.
55-da             Disable assertions.
56
57To read from stdin, set 'in=stdin'.  The format should be specified with an extension, like 'in=stdin.fq.gz'
58To write to stdout, set 'out=stdout'.  The format should be specified with an extension, like 'out=stdout.fasta'
59
60Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
61"
62}
63
64#This block allows symlinked shellscripts to correctly set classpath.
65pushd . > /dev/null
66DIR="${BASH_SOURCE[0]}"
67while [ -h "$DIR" ]; do
68  cd "$(dirname "$DIR")"
69  DIR="$(readlink "$(basename "$DIR")")"
70done
71cd "$(dirname "$DIR")"
72DIR="$(pwd)/"
73popd > /dev/null
74
75#DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
76CP="$DIR""current/"
77
78z="-Xmx800m"
79set=0
80
81if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
82	usage
83	exit
84fi
85
86calcXmx () {
87	source "$DIR""/calcmem.sh"
88	setEnvironment
89	parseXmx "$@"
90	if [[ $set == 1 ]]; then
91		return
92	fi
93	freeRam 800m 84
94	z="-Xmx${RAM}m"
95	z2="-Xms${RAM}m"
96}
97calcXmx "$@"
98
99function filterbyname() {
100	local CMD="java $EA $EOOM $z -cp $CP driver.FilterReadsByName $@"
101	echo $CMD >&2
102	eval $CMD
103}
104
105filterbyname "$@"
106