scbi_multi_gz_reader 0.0.1

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data/.gitignore ADDED
@@ -0,0 +1,14 @@
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+ /.bundle/
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+ /.yardoc
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+ /Gemfile.lock
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+ /_yardoc/
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+ /coverage/
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+ /doc/
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+ /pkg/
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+ /spec/reports/
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+ /tmp/
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+ *.bundle
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+ *.so
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+ *.o
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+ *.a
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+ mkmf.log
data/Gemfile ADDED
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+ source 'https://rubygems.org'
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+
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+ # Specify your gem's dependencies in scbi_multi_gz_reader.gemspec
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+ gemspec
data/LICENSE.txt ADDED
@@ -0,0 +1,22 @@
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+ Copyright (c) 2014 dariogf
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+
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+ MIT License
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+
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+ Permission is hereby granted, free of charge, to any person obtaining
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+ a copy of this software and associated documentation files (the
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+ "Software"), to deal in the Software without restriction, including
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+ without limitation the rights to use, copy, modify, merge, publish,
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+ distribute, sublicense, and/or sell copies of the Software, and to
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+ permit persons to whom the Software is furnished to do so, subject to
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+ the following conditions:
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+
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+ The above copyright notice and this permission notice shall be
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+ included in all copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
18
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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+ LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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+ OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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+ WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
data/README.md ADDED
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+ # ScbiMultiGzReader
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+
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+ Zlib::GzipReader is not able to read multiple stream gz/gzip files, instead it only reads the first stream and then closes the file without warnings so you only get a part of the file when you expected to get the full one.
4
+
5
+ This is a wrapper to read gz/gzip files composed of multiple streams (eg, made by doing a cat to join some gz files in a bigger one.
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+
7
+ By now it only has the readline and eof? instance methods, the ones needed by scbi_fastq to read fastq files.
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+
9
+
10
+ ## Installation
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+
12
+ Add this line to your application's Gemfile:
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+
14
+ ```ruby
15
+ gem 'scbi_multi_gz_reader'
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+ ```
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+
18
+ And then execute:
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+
20
+ $ bundle
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+
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+ Or install it yourself as:
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+
24
+ $ gem install scbi_multi_gz_reader
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+
26
+ ## Usage
27
+
28
+ # read checking for eof
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+
30
+ file=MultiGzReader.new('file.gz'))
31
+
32
+ while !file.eof? do
33
+ puts file.readline
34
+ end
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+
36
+ file.close
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+
38
+ ------
39
+
40
+ # read checking for res.nil?
41
+ file=MultiGzReader.new('file.gz'))
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+
43
+ loop do
44
+ res=file.readline
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+ break if res.nil?
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+ puts res
47
+ end
48
+
49
+ file.close
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+
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+
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+ ## Contributing
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+
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+ 1. Fork it ( https://github.com/[my-github-username]/scbi_multi_gz_reader/fork )
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+ 2. Create your feature branch (`git checkout -b my-new-feature`)
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+ 3. Commit your changes (`git commit -am 'Add some feature'`)
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+ 4. Push to the branch (`git push origin my-new-feature`)
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+ 5. Create a new Pull Request
data/Rakefile ADDED
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+ require "bundler/gem_tasks"
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+
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+
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+ require 'rake/testtask'
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+
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+ Rake::TestTask.new do |t|
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+ t.libs << 'test'
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+ t.pattern = "test/*_test.rb"
9
+ end
@@ -0,0 +1,51 @@
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+ require 'zlib'
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+
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+ class MultiGzReader
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+
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+ def initialize(file_name)
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+ @file = File.open(file_name)
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+ @io = Zlib::GzipReader.new @file
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+ end
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+
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+ def readline
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+
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+ res=nil
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+
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+ begin
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+ res=@io.readline
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+ rescue EOFError => e
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+
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+ #reached END, check if there is more data to read
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+ unused = @io.unused
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+
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+ @io.finish
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+
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+ # there is something left to read, open another stream
24
+ if !unused.nil?
25
+ #puts "FIN1, fpos: #{@file.pos}, unused: #{unused.length}, io_eof: #{@io.eof}, eof: #{@file.eof}"
26
+
27
+ @file.pos -= unused.length
28
+ @io = Zlib::GzipReader.new @file
29
+ #repeat the read so there is no eof error
30
+ res=readline
31
+
32
+ else
33
+ #no more data to read, return nil
34
+ res=nil
35
+ end
36
+ end
37
+
38
+ return res
39
+ end
40
+
41
+ def eof?
42
+ #nothing more to read
43
+ @io.unused.nil? && (@io.closed? || @io.eof?) && (@file.closed? || @file.eof?)
44
+ end
45
+
46
+ def close
47
+ #@io.finish
48
+ @file.close
49
+ end
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+
51
+ end
@@ -0,0 +1,3 @@
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+ module ScbiMultiGzReader
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+ VERSION = "0.0.1"
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+ end
@@ -0,0 +1,6 @@
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+ require "scbi_multi_gz_reader/version"
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+ require "scbi_multi_gz_reader/multi_gz_reader"
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+
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+ module ScbiMultiGzReader
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+ # Your code goes here...
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+ end
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+ # coding: utf-8
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+ lib = File.expand_path('../lib', __FILE__)
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+ $LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
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+ require 'scbi_multi_gz_reader/version'
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+
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+ Gem::Specification.new do |spec|
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+ spec.name = "scbi_multi_gz_reader"
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+ spec.version = ScbiMultiGzReader::VERSION
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+ spec.authors = ["dariogf"]
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+ spec.email = ["dariogf@scbi.uma.es"]
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+ spec.summary = %q{Reads gz/gzip files with multiple streams in ruby}
12
+ spec.description = %q{Wrapper to read gz/gzip files composed of multiple gz streams (eg, made by doing a cat to join some gz files in a bigger one.)}
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+ spec.homepage = ""
14
+ spec.license = "MIT"
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+
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+ spec.files = `git ls-files -z`.split("\x0")
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+ spec.executables = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
18
+ spec.test_files = spec.files.grep(%r{^(test|spec|features)/})
19
+ spec.require_paths = ["lib"]
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+
21
+ spec.add_development_dependency "bundler", "~> 1.7"
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+ spec.add_development_dependency "rake", "~> 10.0"
23
+ end
Binary file
@@ -0,0 +1,194 @@
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+ #!/usr/local/bin/perl -w
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+
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+ # Author: lh3
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+
5
+ use strict;
6
+ use warnings;
7
+ use Getopt::Std;
8
+
9
+ my $usage = qq(
10
+ Usage: fq_all2std.pl <command> <in.txt>
11
+
12
+ Command: scarf2std Convert SCARF format to the standard/Sanger FASTQ
13
+ fqint2std Convert FASTQ-int format to the standard/Sanger FASTQ
14
+ sol2std Convert Solexa/Illumina FASTQ to the standard FASTQ
15
+ fa2std Convert FASTA to the standard FASTQ
16
+ fq2fa Convert various FASTQ-like format to FASTA
17
+ instruction Explanation to different format
18
+ example Show examples of various formats
19
+
20
+ Note: Read/quality sequences MUST be presented in one line.
21
+ \n);
22
+
23
+ die($usage) if (@ARGV < 1);
24
+
25
+ # Solexa->Sanger quality conversion table
26
+ my @conv_table;
27
+ for (-64..64) {
28
+ $conv_table[$_+64] = chr(int(33 + 10*log(1+10**($_/10.0))/log(10)+.499));
29
+ }
30
+
31
+ # parsing command line
32
+ my $cmd = shift;
33
+ my %cmd_hash = (scarf2std=>\&scarf2std, fqint2std=>\&fqint2std, sol2std=>\&sol2std, fa2std=>\&fa2std,
34
+ fq2fa=>\&fq2fa, example=>\&example, instruction=>\&instruction);
35
+ if (defined($cmd_hash{$cmd})) {
36
+ &{$cmd_hash{$cmd}};
37
+ } else {
38
+ die("** Unrecognized command $cmd");
39
+ }
40
+
41
+ sub fa2std {
42
+ my %opts = (q=>25);
43
+ getopts('q:', \%opts);
44
+ my $q = chr($opts{q} + 33);
45
+ warn("-- The default quality is set to $opts{q}. Use '-q' at the command line to change the default.\n");
46
+ while (<>) {
47
+ if (/^>(\S+)/) {
48
+ print "\@$1\n";
49
+ $_ = <>;
50
+ print "$_+\n", $q x (length($_)-1), "\n";
51
+ }
52
+ }
53
+ }
54
+
55
+ sub fq2fa {
56
+ while (<>) {
57
+ if (/^@(\S+)/) {
58
+ print ">$1\n";
59
+ $_ = <>; print;
60
+ <>; <>;
61
+ }
62
+ }
63
+ }
64
+
65
+ sub scarf2std {
66
+ while (<>) {
67
+ my @t = split(':', $_);
68
+ my $name = join('_', @t[0..4]);
69
+ print "\@$name\n$t[5]\n+\n";
70
+ my $qual = '';
71
+ @t = split(/\s/, $t[6]);
72
+ $qual .= $conv_table[$_+64] for (@t);
73
+ print "$qual\n";
74
+ }
75
+ }
76
+
77
+ sub fqint2std {
78
+ while (<>) {
79
+ if (/^@/) {
80
+ print;
81
+ $_ = <>; print; $_ = <>; $_ = <>;
82
+ my @t = split;
83
+ my $qual = '';
84
+ $qual .= $conv_table[$_+64] for (@t);
85
+ print "+\n$qual\n";
86
+ }
87
+ }
88
+ }
89
+
90
+ sub sol2std {
91
+ my $max = 0;
92
+ while (<>) {
93
+ if (/^@/) {
94
+ print;
95
+ $_ = <>; print; $_ = <>; $_ = <>;
96
+ my @t = split('', $_);
97
+ my $qual = '';
98
+ $qual .= $conv_table[ord($_)] for (@t);
99
+ print "+\n$qual\n";
100
+ }
101
+ }
102
+ }
103
+
104
+ sub instruction {
105
+
106
+ print "
107
+ FASTQ format is first used in the Sanger Institute, and therefore
108
+ we take the Sanger specification as the standard FASTQ. Although
109
+ Solexa/Illumina reads file looks pretty much like the standard
110
+ FASTQ, they are different in that the qualities are scaled
111
+ differently. In the quality string, if you can see a character
112
+ with its ASCII code higher than 90, probably your file is in the
113
+ Solexa/Illumina format.
114
+
115
+ Sometimes we also use an integer, instead of a single character,
116
+ to explicitly show the qualities. In that case, negative
117
+ qualities indicates that Solexa/Illumina qualities are used.
118
+
119
+ ";
120
+
121
+ }
122
+
123
+ sub example {
124
+ my $exam_scarf = '
125
+ USI-EAS50_1:4:2:710:120:GTCAAAGTAATAATAGGAGATTTGAGCTATTT:23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 19 23 23 23 18 23 23 23
126
+ USI-EAS50_1:4:2:690:87:GTTTTTTTTTTTCTTTCCATTAATTTCCCTTT:23 23 23 23 23 23 23 23 23 23 23 23 12 23 23 23 23 23 16 23 23 9 18 23 23 23 12 23 18 23 23 23
127
+ USI-EAS50_1:4:2:709:32:GAGAAGTCAAACCTGTGTTAGAAATTTTATAC:23 23 23 23 23 23 23 23 20 23 23 23 23 23 23 23 23 23 23 23 23 12 23 18 23 23 23 23 23 23 23 23
128
+ USI-EAS50_1:4:2:886:890:GCTTATTTAAAAATTTACTTGGGGTTGTCTTT:23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23
129
+ USI-EAS50_1:4:2:682:91:GGGTTTCTAGACTAAAGGGATTTAACAAGTTT:23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 20 23 23 23 23 23 23 23 23 23 23 23 18 23 23 23 23
130
+ USI-EAS50_1:4:2:663:928:GAATTTGTTTGAAGAGTGTCATGGTCAGATCT:23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23
131
+ ';
132
+
133
+ my $exam_fqint = '
134
+ @4_1_912_360
135
+ AAGGGGCTAGAGAAACACGTAATGAAGGGAGGACTC
136
+ +4_1_912_360
137
+ 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 21 40 40 40 40 40 40 40 40 40 26 40 40 14 39 40 40
138
+ @4_1_54_483
139
+ TAATAAATGTGCTTCCTTGATGCATGTGCTATGATT
140
+ +4_1_54_483
141
+ 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 16 40 40 40 28 40 40 40 40 40 40 16 40 40 5 40 40
142
+ @4_1_537_334
143
+ ATTGATGATGCTGTGCACCTAGCAAGAAGTTGCATA
144
+ +4_1_537_334
145
+ 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 21 29 40 40 33 40 40 33 40 40 33 31 40 40 40 40 18 26 40 -2
146
+ @4_1_920_361
147
+ AACGGCACAATCCAGGTTGATGCCTACGGCGGGTAC
148
+ +4_1_920_361
149
+ 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 40 40 40 40 40 40 40 40 31 40 40 40 40 40 40 15 5 -1 3
150
+ @4_1_784_155
151
+ AATGCATGCTTCGAATGGCATTCTCTTCAATCACGA
152
+ +4_1_784_155
153
+ 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 31 40 40 40 40 40
154
+ @4_1_595_150
155
+ AAAGACGTGGCCAGATGGGTGGCCAAGTGCCCGACT
156
+ +4_1_595_150
157
+ 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 30 40 40 40 40 40 40 40 40 40 20 40 40 40 40 40 14 40 40
158
+ ';
159
+
160
+ my $exam_sol = '
161
+ @SLXA-B3_649_FC8437_R1_1_1_610_79
162
+ GATGTGCAATACCTTTGTAGAGGAA
163
+ +SLXA-B3_649_FC8437_R1_1_1_610_79
164
+ YYYYYYYYYYYYYYYYYYWYWYYSU
165
+ @SLXA-B3_649_FC8437_R1_1_1_397_389
166
+ GGTTTGAGAAAGAGAAATGAGATAA
167
+ +SLXA-B3_649_FC8437_R1_1_1_397_389
168
+ YYYYYYYYYWYYYYWWYYYWYWYWW
169
+ @SLXA-B3_649_FC8437_R1_1_1_850_123
170
+ GAGGGTGTTGATCATGATGATGGCG
171
+ +SLXA-B3_649_FC8437_R1_1_1_850_123
172
+ YYYYYYYYYYYYYWYYWYYSYYYSY
173
+ @SLXA-B3_649_FC8437_R1_1_1_362_549
174
+ GGAAACAAAGTTTTTCTCAACATAG
175
+ +SLXA-B3_649_FC8437_R1_1_1_362_549
176
+ YYYYYYYYYYYYYYYYYYWWWWYWY
177
+ @SLXA-B3_649_FC8437_R1_1_1_183_714
178
+ GTATTATTTAATGGCATACACTCAA
179
+ +SLXA-B3_649_FC8437_R1_1_1_183_714
180
+ YYYYYYYYYYWYYYYWYWWUWWWQQ
181
+ ';
182
+
183
+ print qq(
184
+ solexa
185
+ ======
186
+ $exam_sol
187
+ scarf
188
+ =====
189
+ $exam_scarf
190
+ fqint
191
+ =====
192
+ $exam_fqint
193
+ );
194
+ }
data/test/gz.rb ADDED
@@ -0,0 +1,11 @@
1
+ require '../lib/scbi_fastq/multi_gz_reader'
2
+
3
+ file=MultiGzReader.new(File.join(File.dirname(__FILE__),'minitest.fastq.gz'))
4
+
5
+ loop do
6
+ res=file.readline
7
+ puts "LINE: #{res}"
8
+ break if res.nil?
9
+ end
10
+
11
+ file.close
data/test/h1.fastq.gz ADDED
Binary file
data/test/h2.fastq.gz ADDED
Binary file
Binary file
Binary file
@@ -0,0 +1,113 @@
1
+ require File.dirname(__FILE__) + '/test_helper.rb'
2
+
3
+ class ScbiMultiGzReaderTest < Test::Unit::TestCase
4
+
5
+ def setup
6
+
7
+ end
8
+
9
+ def test_mini_multi_gz_reader
10
+
11
+ # test a file with multiple gz streams
12
+
13
+ file=MultiGzReader.new(File.join(File.dirname(__FILE__),'minitest.fastq.gz'))
14
+
15
+ i=0
16
+
17
+ loop do
18
+ res=file.readline
19
+ #puts res
20
+ break if res.nil?
21
+ i = i+1
22
+ end
23
+
24
+ file.close
25
+
26
+ assert_equal(28,i)
27
+
28
+ end
29
+
30
+
31
+ def test_mini_multi_gz_reader_EOF_while
32
+
33
+ # test a file with multiple gz streams
34
+
35
+ file=MultiGzReader.new(File.join(File.dirname(__FILE__),'minitest.fastq.gz'))
36
+
37
+ i=0
38
+
39
+ begin
40
+ res=file.readline
41
+ #puts res
42
+ i = i+1
43
+ end while !file.eof?
44
+
45
+ file.close
46
+
47
+ assert_equal(28,i)
48
+
49
+ end
50
+
51
+ def test_mini_multi_gz_reader_EOF_until
52
+
53
+ # test a file with multiple gz streams
54
+
55
+ file=MultiGzReader.new(File.join(File.dirname(__FILE__),'minitest.fastq.gz'))
56
+
57
+ i=0
58
+
59
+ begin
60
+ res=file.readline
61
+ #puts res
62
+ i = i+1
63
+ end until file.eof?
64
+
65
+ file.close
66
+
67
+ assert_equal(28,i)
68
+
69
+ end
70
+
71
+ def test_empty_multi_gz_reader_EOF_until
72
+
73
+ # test a file with multiple gz streams
74
+
75
+ file=MultiGzReader.new(File.join(File.dirname(__FILE__),'empty.fastq.gz'))
76
+
77
+ i=0
78
+
79
+ while !file.eof? do
80
+ res=file.readline
81
+ #puts res
82
+ i = i+1
83
+ end
84
+
85
+ file.close
86
+
87
+ assert_equal(0,i)
88
+
89
+ end
90
+
91
+
92
+ def test_mini_complete_gz
93
+ #test only one gz stream in file
94
+
95
+ file=MultiGzReader.new(File.join(File.dirname(__FILE__),'minitest_full.fastq.gz'))
96
+
97
+ i=0
98
+
99
+ loop do
100
+ res=file.readline
101
+ #puts res
102
+ break if res.nil?
103
+ i = i+1
104
+ end
105
+
106
+ file.close
107
+
108
+ assert_equal(i,28)
109
+
110
+ end
111
+
112
+
113
+ end
@@ -0,0 +1,3 @@
1
+ require 'stringio'
2
+ require 'test/unit'
3
+ require File.dirname(__FILE__) + '/../lib/scbi_multi_gz_reader'
metadata ADDED
@@ -0,0 +1,100 @@
1
+ --- !ruby/object:Gem::Specification
2
+ name: scbi_multi_gz_reader
3
+ version: !ruby/object:Gem::Version
4
+ version: 0.0.1
5
+ platform: ruby
6
+ authors:
7
+ - dariogf
8
+ autorequire:
9
+ bindir: bin
10
+ cert_chain: []
11
+ date: 2014-11-14 00:00:00.000000000 Z
12
+ dependencies:
13
+ - !ruby/object:Gem::Dependency
14
+ name: bundler
15
+ requirement: !ruby/object:Gem::Requirement
16
+ requirements:
17
+ - - "~>"
18
+ - !ruby/object:Gem::Version
19
+ version: '1.7'
20
+ type: :development
21
+ prerelease: false
22
+ version_requirements: !ruby/object:Gem::Requirement
23
+ requirements:
24
+ - - "~>"
25
+ - !ruby/object:Gem::Version
26
+ version: '1.7'
27
+ - !ruby/object:Gem::Dependency
28
+ name: rake
29
+ requirement: !ruby/object:Gem::Requirement
30
+ requirements:
31
+ - - "~>"
32
+ - !ruby/object:Gem::Version
33
+ version: '10.0'
34
+ type: :development
35
+ prerelease: false
36
+ version_requirements: !ruby/object:Gem::Requirement
37
+ requirements:
38
+ - - "~>"
39
+ - !ruby/object:Gem::Version
40
+ version: '10.0'
41
+ description: Wrapper to read gz/gzip files composed of multiple gz streams (eg, made
42
+ by doing a cat to join some gz files in a bigger one.)
43
+ email:
44
+ - dariogf@scbi.uma.es
45
+ executables: []
46
+ extensions: []
47
+ extra_rdoc_files: []
48
+ files:
49
+ - ".gitignore"
50
+ - Gemfile
51
+ - LICENSE.txt
52
+ - README.md
53
+ - Rakefile
54
+ - lib/scbi_multi_gz_reader.rb
55
+ - lib/scbi_multi_gz_reader/multi_gz_reader.rb
56
+ - lib/scbi_multi_gz_reader/version.rb
57
+ - scbi_multi_gz_reader.gemspec
58
+ - test/empty.fastq.gz
59
+ - test/fq_all2std.pl
60
+ - test/gz.rb
61
+ - test/h1.fastq.gz
62
+ - test/h2.fastq.gz
63
+ - test/minitest.fastq.gz
64
+ - test/minitest_full.fastq.gz
65
+ - test/scbi_multi_gz_reader_test.rb
66
+ - test/test_helper.rb
67
+ homepage: ''
68
+ licenses:
69
+ - MIT
70
+ metadata: {}
71
+ post_install_message:
72
+ rdoc_options: []
73
+ require_paths:
74
+ - lib
75
+ required_ruby_version: !ruby/object:Gem::Requirement
76
+ requirements:
77
+ - - ">="
78
+ - !ruby/object:Gem::Version
79
+ version: '0'
80
+ required_rubygems_version: !ruby/object:Gem::Requirement
81
+ requirements:
82
+ - - ">="
83
+ - !ruby/object:Gem::Version
84
+ version: '0'
85
+ requirements: []
86
+ rubyforge_project:
87
+ rubygems_version: 2.2.2
88
+ signing_key:
89
+ specification_version: 4
90
+ summary: Reads gz/gzip files with multiple streams in ruby
91
+ test_files:
92
+ - test/empty.fastq.gz
93
+ - test/fq_all2std.pl
94
+ - test/gz.rb
95
+ - test/h1.fastq.gz
96
+ - test/h2.fastq.gz
97
+ - test/minitest.fastq.gz
98
+ - test/minitest_full.fastq.gz
99
+ - test/scbi_multi_gz_reader_test.rb
100
+ - test/test_helper.rb