scbi_fqbin 0.2.2 → 0.2.3
Sign up to get free protection for your applications and to get access to all the features.
- checksums.yaml +7 -0
- data/.DS_Store +0 -0
- data/.gitignore +14 -0
- data/Gemfile +4 -0
- data/LICENSE.txt +22 -0
- data/{README.rdoc → README.md} +0 -0
- data/Rakefile +8 -28
- data/lib/scbi_fqbin.rb +3 -5
- data/lib/scbi_fqbin/fastabin.rb +411 -0
- data/lib/scbi_fqbin/fastq_file_c.rb +373 -0
- data/lib/scbi_fqbin/fbin_file.rb +1 -1
- data/lib/scbi_fqbin/t.rb +9 -0
- data/lib/scbi_fqbin/t2.rb +12 -0
- data/lib/scbi_fqbin/version.rb +3 -0
- data/lib_fqbin_src.zip +0 -0
- data/lib_fqbin_src/Makefile +66 -0
- data/lib_fqbin_src/fq +0 -0
- data/lib_fqbin_src/fq.c +165 -0
- data/lib_fqbin_src/hash_fqbin +0 -0
- data/lib_fqbin_src/hash_fqbin.c +212 -0
- data/lib_fqbin_src/idx_fqbin +21 -0
- data/lib_fqbin_src/iterate_fqbin +0 -0
- data/lib_fqbin_src/iterate_fqbin.c +136 -0
- data/lib_fqbin_src/lib_fqbin.c +1748 -0
- data/lib_fqbin_src/lib_fqbin.h +194 -0
- data/lib_fqbin_src/mk_fqbin +0 -0
- data/lib_fqbin_src/mk_fqbin.c +138 -0
- data/lib_fqbin_src/other/bwxform.c +915 -0
- data/lib_fqbin_src/other/bwxform.h +74 -0
- data/lib_fqbin_src/other/find_in_index.c +130 -0
- data/lib_fqbin_src/other/hash_fbin_nogzchunks.c +164 -0
- data/lib_fqbin_src/other/idx_fqbin +0 -0
- data/lib_fqbin_src/other/idx_fqbin.c +67 -0
- data/lib_fqbin_src/other/make_hsh.sh +14 -0
- data/lib_fqbin_src/other/rd_extras_fbin.c +45 -0
- data/lib_fqbin_src/read_fq +0 -0
- data/lib_fqbin_src/read_fq.c +143 -0
- data/lib_fqbin_src/read_fqbin +0 -0
- data/lib_fqbin_src/read_fqbin.c +101 -0
- data/lib_fqbin_src/sort_index +9 -0
- data/lib_fqbin_src/test.rb +13 -0
- data/scbi_fqbin.gemspec +25 -0
- data/test/build.rake +15 -0
- data/test/fbinfile +0 -0
- data/test/fbinfile.index +0 -0
- data/test/no_test_fill_file.rb +66 -0
- data/test/old/app.rb +43 -0
- data/test/old/bin/iterate_fastabin.rb +54 -0
- data/test/old/bin/mk_fastabin.rb +22 -0
- data/test/old/bin/rd_fastabin.rb +36 -0
- data/test/old/bin/rd_fq.rb +20 -0
- data/test/old/bioruby.rb +27 -0
- data/test/old/c/Makefile +34 -0
- data/test/old/c/fbin_lib.zip +0 -0
- data/test/old/c/iterate_fbin.c +54 -0
- data/test/old/c/libreria_gz.c +707 -0
- data/test/old/c/libreria_gz.h +127 -0
- data/test/old/c/main.c +86 -0
- data/test/old/c/mk_fbin.c +24 -0
- data/test/old/c/rd_seq_fbin.c +44 -0
- data/test/old/c/test_ffi/a.out +0 -0
- data/test/old/c/test_ffi/app.c +26 -0
- data/test/old/c/test_ffi/app.rb +19 -0
- data/test/old/c/test_ffi/liblibreria_gz.dylib +0 -0
- data/test/old/c/test_ffi/libmylibrary.dylib +0 -0
- data/test/old/c/test_ffi/my_library.rb +23 -0
- data/test/old/c/test_ffi/mylibrary.c +22 -0
- data/test/old/c/test_ffi/mylibrary.h +6 -0
- data/test/old/c/usage_instructions.txt +62 -0
- data/test/old/ext/Makefile +187 -0
- data/test/old/ext/Makefile.dario +34 -0
- data/test/old/ext/extconf.rb +8 -0
- data/test/old/ext/mk_fbin.c +24 -0
- data/test/old/ext/sample/extras.txt +4 -0
- data/{.gemtest → test/old/ext/sample/extras2.txt} +0 -0
- data/test/old/ext/sample/f1.fasta +10 -0
- data/test/old/ext/sample/f1.fasta.qual +10 -0
- data/test/old/ext/sample/f1.fbin +0 -0
- data/test/old/ext/sample/f1.fbin.index +0 -0
- data/test/old/ext/sample/main.c +86 -0
- data/test/old/ext/usage_instructions.txt +62 -0
- data/test/old/t_scbi_fastabin.rb +140 -0
- data/test/read_tests/10-original_sizes.sh +16 -0
- data/test/read_tests/20-fq_time.sh +23 -0
- data/test/read_tests/30-fbin_read_time.sh +23 -0
- data/test/read_tests/40-bsc_read_time.sh +21 -0
- data/test/read_tests/50-fq_time_x4.sh +25 -0
- data/test/read_tests/60-fbin_read_time_x4.sh +24 -0
- data/test/read_tests/70-bsc_read_time_x4.sh +32 -0
- data/test/results_bio_scbi_fasta.txt +11 -0
- data/test/{test_scbi_fbin_file.rb → scbi_fbin_file_test.rb} +0 -0
- data/test/speed.txt +81 -0
- data/test/t_scbi_fasta.rb +12 -0
- data/test/write_tests/10-original_sizes.sh +16 -0
- data/test/write_tests/20-zip_time.sh +17 -0
- data/test/write_tests/30-mk_fbin_time.sh +23 -0
- data/test/write_tests/31-mk_fbin_time_f30.sh +21 -0
- data/test/write_tests/40-gzip_time.sh +16 -0
- data/test/write_tests/41-bsc_time.sh +16 -0
- data/test/write_tests/50-zip_sizes.sh +16 -0
- data/test/write_tests/60-fbin_sizes.sh +17 -0
- data/test/write_tests/61-fbin_sizes_f30.sh +16 -0
- data/test/write_tests/70-gzip_sizes.sh +17 -0
- data/test/write_tests/80-bsc_sizes.sh +17 -0
- data/website/index.html +87 -0
- data/website/index.txt +81 -0
- data/website/javascripts/rounded_corners_lite.inc.js +285 -0
- data/website/stylesheets/screen.css +159 -0
- data/website/template.html.erb +50 -0
- metadata +208 -95
- data/History.txt +0 -19
- data/Manifest.txt +0 -12
- data/PostInstall.txt +0 -7
- data/script/console +0 -10
- data/script/destroy +0 -14
- data/script/generate +0 -14
data/History.txt
DELETED
@@ -1,19 +0,0 @@
|
|
1
|
-
=== 0.2.2 2013-05-09
|
2
|
-
|
3
|
-
Added extra dependencies
|
4
|
-
|
5
|
-
=== 0.2.1 2013-05-09
|
6
|
-
|
7
|
-
* First public release
|
8
|
-
|
9
|
-
=== 0.0.1 2010-05-14
|
10
|
-
|
11
|
-
* 1 major enhancement:
|
12
|
-
* Initial release
|
13
|
-
|
14
|
-
=== 0.1.0 2010-05-31
|
15
|
-
|
16
|
-
* 1 major enhancement:
|
17
|
-
* Added extras to sequences
|
18
|
-
|
19
|
-
|
data/Manifest.txt
DELETED
data/PostInstall.txt
DELETED
data/script/console
DELETED
@@ -1,10 +0,0 @@
|
|
1
|
-
#!/usr/bin/env ruby
|
2
|
-
# File: script/console
|
3
|
-
irb = RUBY_PLATFORM =~ /(:?mswin|mingw)/ ? 'irb.bat' : 'irb'
|
4
|
-
|
5
|
-
libs = " -r irb/completion"
|
6
|
-
# Perhaps use a console_lib to store any extra methods I may want available in the cosole
|
7
|
-
# libs << " -r #{File.dirname(__FILE__) + '/../lib/console_lib/console_logger.rb'}"
|
8
|
-
libs << " -r #{File.dirname(__FILE__) + '/../lib/scbi_fqbin.rb'}"
|
9
|
-
puts "Loading scbi_fqbin gem"
|
10
|
-
exec "#{irb} #{libs} --simple-prompt"
|
data/script/destroy
DELETED
@@ -1,14 +0,0 @@
|
|
1
|
-
#!/usr/bin/env ruby
|
2
|
-
APP_ROOT = File.expand_path(File.join(File.dirname(__FILE__), '..'))
|
3
|
-
|
4
|
-
begin
|
5
|
-
require 'rubigen'
|
6
|
-
rescue LoadError
|
7
|
-
require 'rubygems'
|
8
|
-
require 'rubigen'
|
9
|
-
end
|
10
|
-
require 'rubigen/scripts/destroy'
|
11
|
-
|
12
|
-
ARGV.shift if ['--help', '-h'].include?(ARGV[0])
|
13
|
-
RubiGen::Base.use_component_sources! [:rubygems, :newgem, :newgem_theme, :test_unit]
|
14
|
-
RubiGen::Scripts::Destroy.new.run(ARGV)
|
data/script/generate
DELETED
@@ -1,14 +0,0 @@
|
|
1
|
-
#!/usr/bin/env ruby
|
2
|
-
APP_ROOT = File.expand_path(File.join(File.dirname(__FILE__), '..'))
|
3
|
-
|
4
|
-
begin
|
5
|
-
require 'rubigen'
|
6
|
-
rescue LoadError
|
7
|
-
require 'rubygems'
|
8
|
-
require 'rubigen'
|
9
|
-
end
|
10
|
-
require 'rubigen/scripts/generate'
|
11
|
-
|
12
|
-
ARGV.shift if ['--help', '-h'].include?(ARGV[0])
|
13
|
-
RubiGen::Base.use_component_sources! [:rubygems, :newgem, :newgem_theme, :test_unit]
|
14
|
-
RubiGen::Scripts::Generate.new.run(ARGV)
|