bio-samtools 0.3.1 → 0.3.2

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Files changed (6) hide show
  1. data/VERSION +1 -1
  2. data/bio-samtools.gemspec +2 -1
  3. data/ext/Makefile-bioruby.patch +27 -0
  4. data/ext/mkrf_conf.rb +6 -4
  5. data/lib/bio/db/sam/external/VERSION +1 -1
  6. metadata +19 -18
data/VERSION CHANGED
@@ -1 +1 @@
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- 0.3.1
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+ 0.3.2
data/bio-samtools.gemspec CHANGED
@@ -5,7 +5,7 @@
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  Gem::Specification.new do |s|
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  s.name = %q{bio-samtools}
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- s.version = "0.3.1"
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+ s.version = "0.3.2"
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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 = [%q{Ricardo Ramirez-Gonzalez}, %q{Dan MacLean}, %q{Raoul J.P. Bonnal}]
@@ -93,6 +93,7 @@ Gem::Specification.new do |s|
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  "doc/rdoc-style.css",
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  "doc/tutorial.html",
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  "doc/tutorial.pdf",
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+ "ext/Makefile-bioruby.patch",
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  "ext/mkrf_conf.rb",
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  "lib/bio-samtools.rb",
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  "lib/bio/.DS_Store",
data/ext/Makefile-bioruby.patch ADDED
@@ -0,0 +1,27 @@
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+ --- Makefile 2011-10-27 14:57:06.000000000 +0200
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+ +++ ../Makefile-bioruby 2011-10-27 14:57:41.000000000 +0200
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+ @@ -1,10 +1,11 @@
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+ CC= gcc
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+ -CFLAGS= -g -Wall -O2 #-m64 #-arch ppc
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+ +CFLAGS= -g -Wall -O2 -m64 #-arch ppc
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+ DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1
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+ KNETFILE_O= knetfile.o
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+ LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \
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+ bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o \
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+ - $(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
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+ + $(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o bam_plcmd.o \
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+ + bam2bcf.o bam2bcf_indel.o sample.o bcftools/bcf.o bcftools/bcfutils.o errmod.o bcftools/fet.o
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+ AOBJS= bam_tview.o bam_plcmd.o sam_view.o \
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+ bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \
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+ bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o \
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+ @@ -81,8 +82,8 @@
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+ dylib:
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+ @$(MAKE) cleanlocal; \
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+ case `uname` in \
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+ - Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.so.1-local;; \
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+ - Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.1.dylib-local;; \
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+ + Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.so.1-local;; \
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+ + Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.1.dylib-local ;; \
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+ *) echo 'Unknown OS';; \
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+ esac
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+
data/ext/mkrf_conf.rb CHANGED
@@ -36,12 +36,14 @@ end
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  task :compile do
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  sh "tar xvfj #{SamToolsFile}"
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  cd("samtools-#{Version}") do
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-
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+ sh "patch < ../Makefile-bioruby.patch"
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  case Config::CONFIG['host_os']
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  when /linux/
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- sh "CFLAGS='-g -Wall -O2 -fPIC' make -e"
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+ #sh "CFLAGS='-g -Wall -O2 -fPIC' make -e"
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+ sh "make"
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  cp("libbam.a","#{path_external}")
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- sh "CFLAGS='-g -Wall -O2 -fPIC' make -e libbam.so.1-local"
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+ #sh "CFLAGS='-g -Wall -O2 -fPIC' make -e libbam.so.1-local"
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+ sh "make libbam.so.1-local"
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  cp("libbam.so.1","#{path_external}")
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  when /darwin/
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  sh "make"
@@ -49,7 +51,7 @@ task :compile do
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  sh "make libbam.1.dylib-local"
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  cp("libbam.1.dylib","#{path_external}")
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  when /mswin|mingw/ then raise NotImplementedError, "BWA library is not available for Windows platform"
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- end#case
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+ end #case
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  end #cd
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  end
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data/lib/bio/db/sam/external/VERSION CHANGED
@@ -1 +1 @@
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- 0.1.16
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+ 0.1.18
metadata CHANGED
@@ -1,7 +1,7 @@
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  --- !ruby/object:Gem::Specification
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  name: bio-samtools
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  version: !ruby/object:Gem::Version
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- version: 0.3.1
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+ version: 0.3.2
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  prerelease:
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  platform: ruby
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  authors:
@@ -15,7 +15,7 @@ date: 2011-10-27 00:00:00.000000000Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: ffi
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- requirement: &2169462860 !ruby/object:Gem::Requirement
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+ requirement: &2152165380 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -23,10 +23,10 @@ dependencies:
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  version: '0'
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  type: :runtime
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  prerelease: false
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- version_requirements: *2169462860
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+ version_requirements: *2152165380
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  - !ruby/object:Gem::Dependency
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  name: bio
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- requirement: &2169461340 !ruby/object:Gem::Requirement
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+ requirement: &2152164200 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -34,10 +34,10 @@ dependencies:
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  version: 1.4.2
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  type: :runtime
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  prerelease: false
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- version_requirements: *2169461340
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+ version_requirements: *2152164200
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  - !ruby/object:Gem::Dependency
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  name: shoulda
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- requirement: &2169458620 !ruby/object:Gem::Requirement
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+ requirement: &2152162920 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -45,10 +45,10 @@ dependencies:
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  version: '0'
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  type: :development
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  prerelease: false
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- version_requirements: *2169458620
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+ version_requirements: *2152162920
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  - !ruby/object:Gem::Dependency
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  name: bundler
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- requirement: &2169456540 !ruby/object:Gem::Requirement
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+ requirement: &2152161080 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -56,10 +56,10 @@ dependencies:
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  version: 1.0.0
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  type: :development
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  prerelease: false
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- version_requirements: *2169456540
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+ version_requirements: *2152161080
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  - !ruby/object:Gem::Dependency
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  name: jeweler
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- requirement: &2169454480 !ruby/object:Gem::Requirement
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+ requirement: &2152160280 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -67,10 +67,10 @@ dependencies:
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  version: '0'
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  type: :development
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  prerelease: false
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- version_requirements: *2169454480
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+ version_requirements: *2152160280
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  - !ruby/object:Gem::Dependency
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  name: rcov
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- requirement: &2169453180 !ruby/object:Gem::Requirement
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+ requirement: &2152158920 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -78,10 +78,10 @@ dependencies:
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  version: '0'
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  type: :development
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  prerelease: false
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- version_requirements: *2169453180
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+ version_requirements: *2152158920
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  - !ruby/object:Gem::Dependency
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  name: bio
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- requirement: &2169451320 !ruby/object:Gem::Requirement
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+ requirement: &2152158080 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -89,10 +89,10 @@ dependencies:
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  version: 1.4.2
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  type: :development
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  prerelease: false
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- version_requirements: *2169451320
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+ version_requirements: *2152158080
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  - !ruby/object:Gem::Dependency
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  name: ffi
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- requirement: &2169447120 !ruby/object:Gem::Requirement
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+ requirement: &2152156660 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -100,7 +100,7 @@ dependencies:
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  version: '0'
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  type: :development
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  prerelease: false
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- version_requirements: *2169447120
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+ version_requirements: *2152156660
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  description: ! "Binder of samtools for ruby, on the top of FFI. \n\n This project
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  was born from the need to add support of BAM files to \n the gee_fu genome browser
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  (http://github.com/danmaclean/gee_fu)."
@@ -184,6 +184,7 @@ files:
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  - doc/rdoc-style.css
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  - doc/tutorial.html
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  - doc/tutorial.pdf
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+ - ext/Makefile-bioruby.patch
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  - ext/mkrf_conf.rb
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  - lib/bio-samtools.rb
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  - lib/bio/.DS_Store
@@ -237,7 +238,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
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  version: '0'
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  segments:
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  - 0
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- hash: -3326585484229877040
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+ hash: 1935979892005829555
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  required_rubygems_version: !ruby/object:Gem::Requirement
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  none: false
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  requirements: