htslib 0.0.10 → 0.1.0

data/lib/hts/libhts/cram.rb

@@ -2,296 +2,291 @@
 
 module HTS
   module LibHTS
-
-=begin
-
-attach_function \
-  :cram_fd_get_header,
-  [CramFd],
-  SamHdr.by_ref
-
-attach_function \
-  :cram_fd_set_header,
-  [CramFd, SamHdr.by_ref],
-  :void
-  
-attach_function \
-  :cram_fd_get_version,
-  [CramFd],
-  :int
-
-attach_function \
-  :cram_fd_set_version,
-  [CramFd, :int],
-  :void
-
-attach_function \
-  :cram_major_vers,
-  [CramFd],
-  :int
-
-attach_function \
-  :cram_minor_vers,
-  [CramFd],
-  :int
-
-attach_function \
-  :cram_fd_get_fp,
-  [CramFd],
-  HFile.by_ref
-
-attach_function \
-  :cram_fd_set_fp,
-  [CramFd, HFile],
-  :void
-
-attach_function \
-  :cram_container_get_length,
-  [CramContainer],
-  :int32
-
-attach_function \
-  :cram_container_set_length,
-  [CramContainer, :int32],
-  :void
-
-attach_function \
-  :cram_container_get_num_blocks,
-  [CramContainer],
-  :int32
-
-attach_function \
-  :cram_container_set_num_blocks,
-  [CramContainer, :int32],
-  :void
-  
-attach_function \
-  :cram_container_get_landmarks,
-  [CramContainer, :int32],
-  :pointer
-
-attach_function \
-  :cram_container_set_landmarks,
-  [CramContainer, :Int32, :pointer],
-  :void
-
-attach_function \
-  :cram_container_is_empty,
-  [CramFd],
-  :int
-
-attach_function \
-  :cram_block_get_content_id,
-  [CramBlock],
-  :int32
-
-attach_function \
-  :cram_block_get_comp_size,
-  [CramBlock],
-  :int32
-
-attach_function \
-  :cram_block_get_uncomp_size,
-  [CramBlock],
-  :int32
-
-attach_function \
-  :cram_block_get_crc32,
-  [CramBlock],
-  :int32
-
-attach_function \
-  :cram_block_get_data,
-  [CramBlock],
-  :pointer
-
-attach_function \
-  :cram_block_get_content_type,
-  [CramBlock],
-  CramContentType                # ?
-
-attach_function \
-  :cram_block_set_content_id,
-  [CramBlock, :int32],
-  :void
-  
-attach_function \
-  :cram_block_set_comp_size,
-  [CramBlock, :int32],
-  :void
-
-attach_function \
-  :cram_block_set_uncomp_size,
-  [CramBlock, :int32],
-  :void
-  
-attach_function \
-  :cram_block_set_crc32,
-  [CramBlock, :int32],
-  :void
-
-attach_function \
-  :cram_block_set_data,
-  [CramBlock, :pointer],
-  :void
-
-attach_function \
-  :cram_block_append,
-  [CramBlock, :pointer, :int],
-  :int
-
-attach_function \
-  :cram_block_update_size,
-  [CramBlock],
-  :void
-
-attach_function \
-  :cram_block_get_offset,
-  [CramBlock],
-  :size_t
-
-attach_function \
-  :cram_block_set_offset,
-  [CramBlock, :size_t],
-  :void
-
-attach_function \
-  :cram_block_size,
-  [CramBlock],
-  :uint32
-
-attach_function \
-  :cram_transcode_rg,
-  [CramFd, CramFd, CramContainer, :int, :pointer, :pointer],
-  :int
-
-attach_function \
-  :cram_copy_slice,
-  [CramFd, CramFd, :int32],
-  :int
-
-attach_function \
-  :cram_new_block,
-  [CramContentType, :int],
-  CramBlock
-
-attach_function \
-  :cram_read_block,
-  [CramFd],
-  CramBlock
-
-attach_function \
-  :cram_write_block,
-  [CramFd, CramBlock],
-  :int
-
-attach_function \
-  :cram_free_block,
-  [CramBlock],
-  :void
-  
-attach_function \
-  :cram_uncompress_block,
-  [CramBlock],
-  :int
-
-attach_function \
-  :cram_compress_block,
-  [CramFd, CramBlock, CramMetrics, :int, :int],
-  :int
-
-attach_function \
-  :cram_compress_block2,
-  [CramFd, CramSlice, CramBlock, CramMetrics, :int, :int],
-  :int
-
-attach_function \
-  :cram_new_container,
-  [:int, :int],
-  CramContainer
-
-attach_function \
-  :cram_free_container,
-  [CramContainer],
-  :void
-
-attach_function \
-  :cram_read_container,
-  [CramFd],
-  CramContainer
-
-attach_function \
-  :cram_write_container,
-  [CramFd, CramContainer],
-  :int
-
-attach_function \
-  :cram_store_container,
-  [CramFd, CramContainer, :string, :pointer],
-  :int
-
-attach_function \
-  :cram_container_size,
-  [CramContainer],
-  :int
-
-attach_function \
-  :cram_open,
-  [:string, :string],
-  CramFd
-
-attach_function \
-  :cram_dopen,
-  [:pointer, :string, :string],
-  CramFd
-
-attach_function \
-  :cram_close,
-  [CramFd],
-  :int
-
-=end
-
-attach_function \
-  :cram_seek,
-  [:pointer, :off_t, :int], :int # FIXME pointer should be CramFd
-
-=begin
-
-attach_function \
-  :cram_flush,
-  [CramFd],
-  :int
-
-attach_function \
-  :cram_eof,
-  [CramFd],
-  :int
-
-attach_function \
-  :cram_set_option,
-  [CramFd, HtsFmtOption, ...], # vararg!
-  :int
-
-attach_function \
-  :cram_set_voption,
-  [CramFd, HtsFmtOption, VaList],
-  :int
-
-attach_function \
-  :cram_set_header,
-  [CramFd, SamHdr.by_ref],
-  :int
-
-attach_function \
-  :cram_check_eof = :cram_check_EOF,
-  [CramFd], :int
-
-attach_function \
-  :cram_get_refs,
-  [HtsFile],
-  RefsT # what is RefsT
-
-=end
+    #
+    # attach_function \
+    #   :cram_fd_get_header,
+    #   [CramFd],
+    #   SamHdr.by_ref
+    #
+    # attach_function \
+    #   :cram_fd_set_header,
+    #   [CramFd, SamHdr.by_ref],
+    #   :void
+    #
+    # attach_function \
+    #   :cram_fd_get_version,
+    #   [CramFd],
+    #   :int
+    #
+    # attach_function \
+    #   :cram_fd_set_version,
+    #   [CramFd, :int],
+    #   :void
+    #
+    # attach_function \
+    #   :cram_major_vers,
+    #   [CramFd],
+    #   :int
+    #
+    # attach_function \
+    #   :cram_minor_vers,
+    #   [CramFd],
+    #   :int
+    #
+    # attach_function \
+    #   :cram_fd_get_fp,
+    #   [CramFd],
+    #   HFile.by_ref
+    #
+    # attach_function \
+    #   :cram_fd_set_fp,
+    #   [CramFd, HFile],
+    #   :void
+    #
+    # attach_function \
+    #   :cram_container_get_length,
+    #   [CramContainer],
+    #   :int32
+    #
+    # attach_function \
+    #   :cram_container_set_length,
+    #   [CramContainer, :int32],
+    #   :void
+    #
+    # attach_function \
+    #   :cram_container_get_num_blocks,
+    #   [CramContainer],
+    #   :int32
+    #
+    # attach_function \
+    #   :cram_container_set_num_blocks,
+    #   [CramContainer, :int32],
+    #   :void
+    #
+    # attach_function \
+    #   :cram_container_get_landmarks,
+    #   [CramContainer, :int32],
+    #   :pointer
+    #
+    # attach_function \
+    #   :cram_container_set_landmarks,
+    #   [CramContainer, :Int32, :pointer],
+    #   :void
+    #
+    # attach_function \
+    #   :cram_container_is_empty,
+    #   [CramFd],
+    #   :int
+    #
+    # attach_function \
+    #   :cram_block_get_content_id,
+    #   [CramBlock],
+    #   :int32
+    #
+    # attach_function \
+    #   :cram_block_get_comp_size,
+    #   [CramBlock],
+    #   :int32
+    #
+    # attach_function \
+    #   :cram_block_get_uncomp_size,
+    #   [CramBlock],
+    #   :int32
+    #
+    # attach_function \
+    #   :cram_block_get_crc32,
+    #   [CramBlock],
+    #   :int32
+    #
+    # attach_function \
+    #   :cram_block_get_data,
+    #   [CramBlock],
+    #   :pointer
+    #
+    # attach_function \
+    #   :cram_block_get_content_type,
+    #   [CramBlock],
+    #   CramContentType                # ?
+    #
+    # attach_function \
+    #   :cram_block_set_content_id,
+    #   [CramBlock, :int32],
+    #   :void
+    #
+    # attach_function \
+    #   :cram_block_set_comp_size,
+    #   [CramBlock, :int32],
+    #   :void
+    #
+    # attach_function \
+    #   :cram_block_set_uncomp_size,
+    #   [CramBlock, :int32],
+    #   :void
+    #
+    # attach_function \
+    #   :cram_block_set_crc32,
+    #   [CramBlock, :int32],
+    #   :void
+    #
+    # attach_function \
+    #   :cram_block_set_data,
+    #   [CramBlock, :pointer],
+    #   :void
+    #
+    # attach_function \
+    #   :cram_block_append,
+    #   [CramBlock, :pointer, :int],
+    #   :int
+    #
+    # attach_function \
+    #   :cram_block_update_size,
+    #   [CramBlock],
+    #   :void
+    #
+    # attach_function \
+    #   :cram_block_get_offset,
+    #   [CramBlock],
+    #   :size_t
+    #
+    # attach_function \
+    #   :cram_block_set_offset,
+    #   [CramBlock, :size_t],
+    #   :void
+    #
+    # attach_function \
+    #   :cram_block_size,
+    #   [CramBlock],
+    #   :uint32
+    #
+    # attach_function \
+    #   :cram_transcode_rg,
+    #   [CramFd, CramFd, CramContainer, :int, :pointer, :pointer],
+    #   :int
+    #
+    # attach_function \
+    #   :cram_copy_slice,
+    #   [CramFd, CramFd, :int32],
+    #   :int
+    #
+    # attach_function \
+    #   :cram_new_block,
+    #   [CramContentType, :int],
+    #   CramBlock
+    #
+    # attach_function \
+    #   :cram_read_block,
+    #   [CramFd],
+    #   CramBlock
+    #
+    # attach_function \
+    #   :cram_write_block,
+    #   [CramFd, CramBlock],
+    #   :int
+    #
+    # attach_function \
+    #   :cram_free_block,
+    #   [CramBlock],
+    #   :void
+    #
+    # attach_function \
+    #   :cram_uncompress_block,
+    #   [CramBlock],
+    #   :int
+    #
+    # attach_function \
+    #   :cram_compress_block,
+    #   [CramFd, CramBlock, CramMetrics, :int, :int],
+    #   :int
+    #
+    # attach_function \
+    #   :cram_compress_block2,
+    #   [CramFd, CramSlice, CramBlock, CramMetrics, :int, :int],
+    #   :int
+    #
+    # attach_function \
+    #   :cram_new_container,
+    #   [:int, :int],
+    #   CramContainer
+    #
+    # attach_function \
+    #   :cram_free_container,
+    #   [CramContainer],
+    #   :void
+    #
+    # attach_function \
+    #   :cram_read_container,
+    #   [CramFd],
+    #   CramContainer
+    #
+    # attach_function \
+    #   :cram_write_container,
+    #   [CramFd, CramContainer],
+    #   :int
+    #
+    # attach_function \
+    #   :cram_store_container,
+    #   [CramFd, CramContainer, :string, :pointer],
+    #   :int
+    #
+    # attach_function \
+    #   :cram_container_size,
+    #   [CramContainer],
+    #   :int
+    #
+    # attach_function \
+    #   :cram_open,
+    #   [:string, :string],
+    #   CramFd
+    #
+    # attach_function \
+    #   :cram_dopen,
+    #   [:pointer, :string, :string],
+    #   CramFd
+    #
+    # attach_function \
+    #   :cram_close,
+    #   [CramFd],
+    #   :int
+    #
+
+    attach_function \
+      :cram_seek,
+      %i[pointer off_t int], :int # FIXME: pointer should be CramFd
+
+    #
+    # attach_function \
+    #   :cram_flush,
+    #   [CramFd],
+    #   :int
+    #
+    # attach_function \
+    #   :cram_eof,
+    #   [CramFd],
+    #   :int
+    #
+    # attach_function \
+    #   :cram_set_option,
+    #   [CramFd, HtsFmtOption, ...], # vararg!
+    #   :int
+    #
+    # attach_function \
+    #   :cram_set_voption,
+    #   [CramFd, HtsFmtOption, VaList],
+    #   :int
+    #
+    # attach_function \
+    #   :cram_set_header,
+    #   [CramFd, SamHdr.by_ref],
+    #   :int
+    #
+    # attach_function \
+    #   :cram_check_eof = :cram_check_EOF,
+    #   [CramFd], :int
+    #
+    # attach_function \
+    #   :cram_get_refs,
+    #   [HtsFile],
+    #   RefsT # what is RefsT
+    #
   end
-end
+end

data/lib/hts/libhts/vcf.rb

@@ -221,6 +221,20 @@ module HTS
           LibHTS::BcfIdpair.size * int_id # offset
         )[:val][:info][type] >> 12
       end
+
+      def bcf_hdr_id2type(hdr, type, int_id)
+        LibHTS::BcfIdpair.new(
+          hdr[:id][LibHTS::BCF_DT_ID].to_ptr +
+          LibHTS::BcfIdpair.size * int_id # offset
+        )[:val][:info][type] >> 4 & 0xf
+      end
+
+      def bcf_hdr_id2coltype(hdr, type, int_id)
+        LibHTS::BcfIdpair.new(
+          hdr[:id][LibHTS::BCF_DT_ID].to_ptr +
+          LibHTS::BcfIdpair.size * int_id # offset
+        )[:val][:info][type] & 0xf
+      end
     end
   end
 end

data/lib/hts/libhts.rb

@@ -1,6 +1,7 @@
 # frozen_string_literal: true
 
 require_relative "ffi_ext/struct"
+require_relative "ffi_ext/pointer"
 
 module HTS
   module LibHTS
@@ -12,6 +13,9 @@ module HTS
       raise LoadError, "#{e}\nCould not find #{HTS.lib_path}"
     end
 
+    # @!macro attach_function
+    #   @!method $1(${2--2})
+    #   @return [${-1}] the return value of $0
     def self.attach_function(*)
       super
     rescue FFI::NotFoundError => e

data/lib/hts/{tabix.rb → tbx.rb}

@@ -1,9 +1,11 @@
+# frozen_string_literal: true
+
 require_relative "../htslib"
 
 require_relative "hts"
 
 module HTS
-  class Tabix < Hts
+  class Tbx < Hts
     include Enumerable
 
     attr_reader :file_name
@@ -22,7 +24,7 @@ module HTS
 
     def initialize(file_name, threads: nil)
       if block_given?
-        message = "HTS::Tabix.new() dose not take block; Please use HTS::Tabix.open() instead"
+        message = "HTS::Tbx.new() dose not take block; Please use HTS::Tbx.open() instead"
         raise message
       end
 
@@ -40,14 +42,5 @@ module HTS
         raise "Failed to set number of threads: #{threads}" if r < 0
       end
     end
-
-    def close
-      LibHTS.hts_close(@hts_file)
-      @hts_file = nil
-    end
-
-    def closed?
-      @hts_file.nil?
-    end
   end
 end

data/lib/hts/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module HTS
-  VERSION = "0.0.10"
+  VERSION = "0.1.0"
 end

data/lib/htslib.rb

@@ -40,6 +40,6 @@ module HTS
 
   autoload :Bam,    "hts/bam"
   autoload :Bcf,    "hts/bcf"
-  autoload :Tabix,  "hts/tabix"
+  autoload :Tbx,    "hts/tbx"
   autoload :Faidx,  "hts/faidx"
 end