bio-bwa 0.2.1 → 0.2.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/VERSION +1 -1
- data/bio-bwa.gemspec +2 -3
- data/lib/bio/bwa.rb +3 -3
- metadata +3 -4
- data/ext/bwt_gen/Makefile +0 -23
data/VERSION
CHANGED
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@@ -1 +1 @@
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1
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-
0.2.
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1
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+
0.2.2
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data/bio-bwa.gemspec
CHANGED
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@@ -5,11 +5,11 @@
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Gem::Specification.new do |s|
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s.name = %q{bio-bwa}
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-
s.version = "0.2.
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8
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+
s.version = "0.2.2"
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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s.authors = ["Francesco Strozzi"]
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-
s.date = %q{2011-
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+
s.date = %q{2011-04-15}
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s.description = %q{Ruby binding for BWA mapping software, built using Ruby-FFI library}
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s.email = %q{francesco.strozzi@gmail.com}
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s.extensions = ["ext/mkrf_conf.rb"]
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@@ -59,7 +59,6 @@ Gem::Specification.new do |s|
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"ext/bwaseqio.c",
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"ext/bwt.c",
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"ext/bwt.h",
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-
"ext/bwt_gen/Makefile",
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"ext/bwt_gen/QSufSort.c",
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"ext/bwt_gen/QSufSort.h",
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"ext/bwt_gen/bwt_gen.c",
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data/lib/bio/bwa.rb
CHANGED
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@@ -9,7 +9,7 @@ module Bio
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# @option params [String] :file_in the Fasta or FastQ file (REQUIRED)
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# @option params [String] :prefix the prefix name for the PAC file
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def self.fa2pac(params={})
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valid_params = %
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+
valid_params = %w(file_in prefix)
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last_params = [:file_in, :prefix]
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mandatory_params = [:file_in]
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check_mandatory(mandatory_params, params)
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@@ -22,7 +22,7 @@ module Bio
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# @option params [String] :file_in the PAC file (REQUIRED)
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# @option params [String] :file_out the name of the BWT file (REQUIRED)
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def self.pac2bwt(params={})
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valid_params = %
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valid_params = %w(file_in file_out)
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last_params = [:file_in,:file_out]
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check_mandatory(last_params, params)
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args = build_parameters("pac2bwt",valid_params,params,last_params)
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@@ -58,7 +58,7 @@ module Bio
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# @option params [String] :file_in the PAC file (REQUIRED)
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# @option params [String] :file_out the name of the REV PAC (REQUIRED)
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def self.bwt2sa(params={})
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valid_params = %
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valid_params = %w(file_in file_out i)
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last_params = [:file_in,:file_out]
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check_mandatory(last_params, params)
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args = build_parameters("bwt2sa",valid_params,params,last_params)
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metadata
CHANGED
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@@ -2,7 +2,7 @@
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name: bio-bwa
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version: !ruby/object:Gem::Version
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prerelease:
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version: 0.2.
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version: 0.2.2
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platform: ruby
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authors:
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- Francesco Strozzi
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@@ -10,7 +10,7 @@ autorequire:
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bindir: bin
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cert_chain: []
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date: 2011-
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date: 2011-04-15 00:00:00 +02:00
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default_executable:
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dependencies:
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- !ruby/object:Gem::Dependency
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@@ -130,7 +130,6 @@ files:
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- ext/bwaseqio.c
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- ext/bwt.c
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- ext/bwt.h
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-
- ext/bwt_gen/Makefile
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- ext/bwt_gen/QSufSort.c
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- ext/bwt_gen/QSufSort.h
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- ext/bwt_gen/bwt_gen.c
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@@ -193,7 +192,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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-
hash:
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+
hash: -2614376083052286076
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segments:
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- 0
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version: "0"
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data/ext/bwt_gen/Makefile
DELETED
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@@ -1,23 +0,0 @@
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1
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CC= gcc
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CFLAGS= -g -Wall -O2 -m64 # comment out `-m64' for 32-bit compilation
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DFLAGS= -D_FILE_OFFSET_BITS=64
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OBJS= bwt_gen.o QSufSort.o
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INCLUDES=
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VERSION= 0.1.0
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LIBS=
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SUBDIRS=
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.SUFFIXES:.c .o
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.c.o:
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$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
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-
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lib:libbwtgen.a
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-
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libbwtgen.a:$(OBJS)
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$(AR) -cru $@ $(OBJS)
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-
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cleanlocal:
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rm -f gmon.out *.o a.out $(PROG) *~ *.a
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-
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clean:cleanlocal
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