bio-bwa 0.2.1 → 0.2.2

data/VERSION

@@ -1 +1 @@
-0.2.1
+0.2.2

data/bio-bwa.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{bio-bwa}
-  s.version = "0.2.1"
+  s.version = "0.2.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Francesco Strozzi"]
-  s.date = %q{2011-03-22}
+  s.date = %q{2011-04-15}
   s.description = %q{Ruby binding for BWA mapping software, built using Ruby-FFI library}
   s.email = %q{francesco.strozzi@gmail.com}
   s.extensions = ["ext/mkrf_conf.rb"]
@@ -59,7 +59,6 @@ Gem::Specification.new do |s|
     "ext/bwaseqio.c",
     "ext/bwt.c",
     "ext/bwt.h",
-    "ext/bwt_gen/Makefile",
     "ext/bwt_gen/QSufSort.c",
     "ext/bwt_gen/QSufSort.h",
     "ext/bwt_gen/bwt_gen.c",

data/lib/bio/bwa.rb

@@ -9,7 +9,7 @@ module Bio
       # @option params [String] :file_in the Fasta or FastQ file (REQUIRED)
       # @option params [String] :prefix the prefix name for the PAC file
       def self.fa2pac(params={})
-        valid_params = %q(file_in prefix)
+        valid_params = %w(file_in prefix)
         last_params = [:file_in, :prefix]
         mandatory_params = [:file_in]
         check_mandatory(mandatory_params, params)
@@ -22,7 +22,7 @@ module Bio
       # @option params [String] :file_in the PAC file (REQUIRED)
       # @option params [String] :file_out the name of the BWT file (REQUIRED)
       def self.pac2bwt(params={})
-        valid_params = %q(file_in file_out)
+        valid_params = %w(file_in file_out)
         last_params = [:file_in,:file_out]
         check_mandatory(last_params, params)
         args = build_parameters("pac2bwt",valid_params,params,last_params)
@@ -58,7 +58,7 @@ module Bio
       # @option params [String] :file_in the PAC file (REQUIRED)
       # @option params [String] :file_out the name of the REV PAC (REQUIRED)
       def self.bwt2sa(params={})
-        valid_params = %q(file_in file_out i)
+        valid_params = %w(file_in file_out i)
         last_params = [:file_in,:file_out]
         check_mandatory(last_params, params)
         args = build_parameters("bwt2sa",valid_params,params,last_params)

metadata

@@ -2,7 +2,7 @@
 name: bio-bwa
 version: !ruby/object:Gem::Version 
   prerelease: 
-  version: 0.2.1
+  version: 0.2.2
 platform: ruby
 authors: 
 - Francesco Strozzi
@@ -10,7 +10,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-03-22 00:00:00 +01:00
+date: 2011-04-15 00:00:00 +02:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -130,7 +130,6 @@ files:
 - ext/bwaseqio.c
 - ext/bwt.c
 - ext/bwt.h
-- ext/bwt_gen/Makefile
 - ext/bwt_gen/QSufSort.c
 - ext/bwt_gen/QSufSort.h
 - ext/bwt_gen/bwt_gen.c
@@ -193,7 +192,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
-      hash: 4340680635889925371
+      hash: -2614376083052286076
       segments: 
       - 0
       version: "0"

data/ext/bwt_gen/Makefile

@@ -1,23 +0,0 @@
-CC=			gcc
-CFLAGS=		-g -Wall -O2 -m64 # comment out `-m64' for 32-bit compilation
-DFLAGS=		-D_FILE_OFFSET_BITS=64
-OBJS=		bwt_gen.o QSufSort.o
-INCLUDES=	
-VERSION=	0.1.0
-LIBS=		
-SUBDIRS=
-
-.SUFFIXES:.c .o
-
-.c.o:
-		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
-
-lib:libbwtgen.a
-
-libbwtgen.a:$(OBJS)
-		$(AR) -cru $@ $(OBJS)
-
-cleanlocal:
-		rm -f gmon.out *.o a.out $(PROG) *~ *.a
-
-clean:cleanlocal