htslib 0.0.4 → 0.0.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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+  data.tar.gz: c90ad39aa4919cefa56e534a706bf9659bba9c6ad69eb374491092ce16ae93f6
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+  data.tar.gz: 9cc235f8876b8fd4339593eb84a0f2cb8b605b9c82b624cd0f97691b4109a672f55ae90447bba17fb5efcb8257279ad8c2d87234bca390b1624c7aa8f9a7014e

data/lib/hts/bam/record.rb

@@ -21,6 +21,8 @@ module HTS
         @bam1.to_ptr
       end
 
+      attr_reader :header
+
       # def initialize_copy
       #   super
       # end
@@ -161,6 +163,23 @@ module HTS
         Flag.new(@bam1[:core][:flag])
       end
 
+      def tag(str)
+        aux = LibHTS.bam_aux_get(@bam1, str)
+        return nil if aux.null?
+
+        t = aux.read_string(1)
+        case t
+        when "i", "I", "c", "C", "s", "S"
+          LibHTS.bam_aux2i(aux)
+        when "f", "d"
+          LibHTS.bam_aux2f(aux)
+        when "Z", "H"
+          LibHTS.bam_aux2Z(aux)
+        when "A"
+          LibHTS.bam_aux2A(aux)
+        end
+      end
+
       def to_s
         kstr = LibHTS::KString.new
         raise "Failed to format bam record" if LibHTS.sam_format1(@header.struct, @bam1, kstr) == -1

data/lib/hts/bam.rb

@@ -7,12 +7,10 @@ require_relative "bam/header"
 require_relative "bam/cigar"
 require_relative "bam/flag"
 require_relative "bam/record"
-require_relative "utils/open_method"
 
 module HTS
   class Bam
     include Enumerable
-    extend Utils::OpenMethod
 
     attr_reader :file_path, :mode, :header
     # HtfFile is FFI::BitStruct
@@ -35,9 +33,6 @@ module HTS
       @htf_file  = LibHTS.hts_open(file_path, mode)
       @header    = Bam::Header.new(LibHTS.sam_hdr_read(htf_file))
 
-      # FIXME: should be defined here?
-      @bam1      = LibHTS.bam_init1
-
       # read
       if mode[0] == "r"
         # load index
@@ -87,24 +82,29 @@ module HTS
       # LibHTS.bgzf_flush(@htf_file.fp.bgzf)
     end
 
-    def each(&block)
+    def each
       # Each does not always start at the beginning of the file.
       # This is the common behavior of IO objects in Ruby.
       # This may change in the future.
-      while LibHTS.sam_read1(htf_file, header, @bam1) > 0
-        record = Record.new(@bam1, header)
-        block.call(record)
+      return to_enum(__method__) unless block_given?
+
+      while LibHTS.sam_read1(htf_file, header, bam1 = LibHTS.bam_init1) > 0
+        record = Record.new(bam1, header)
+        yield record
       end
+      self
     end
 
     # query [WIP]
     def query(region)
       qiter = LibHTS.sam_itr_querys(@idx, header, region)
       begin
-        slen = LibHTS.sam_itr_next(htf_file, qiter, @bam1)
+        bam1 = LibHTS.bam_init1
+        slen = LibHTS.sam_itr_next(htf_file, qiter, bam1)
         while slen > 0
-          yield Record.new(@bam1, header)
-          slen = LibHTS.sam_itr_next(htf_file, qiter, @bam1)
+          yield Record.new(bam1, header)
+          bam1 = LibHTS.bam_init1
+          slen = LibHTS.sam_itr_next(htf_file, qiter, bam1)
         end
       ensure
         LibHTS.hts_itr_destroy(qiter)

data/lib/hts/bcf/info.rb

@@ -7,6 +7,7 @@ module HTS
         @record = record
       end
 
+      # @note Specify the type. If you don't specify a type, it will still work, but it will be slower.
       def get(key, type = nil)
         n = FFI::MemoryPointer.new(:int)
         p1 = @record.p1
@@ -20,19 +21,71 @@ module HTS
           p1.read_pointer
         end
 
-        case type.to_sym
+        type ||= info_type_to_string(get_info_type(key))
+
+        case type&.to_sym
         when :int, :int32
           info_values.call(LibHTS::BCF_HT_INT)
                      .read_array_of_int32(n.read_int)
         when :float, :real
           info_values.call(LibHTS::BCF_HT_REAL)
                      .read_array_of_float(n.read_int)
-        when :flag
-          info_values.call(LibHTS::BCF_HT_FLAG)
-                     .read_int == 1
+        when :flag, :bool
+          case ret = LibHTS.bcf_get_info_flag(h, r, key, p1, n)
+          when 1 then true
+          when 0 then false
+          when -1 then nil
+          else
+            raise "Unknown return value from bcf_get_info_flag: #{ret}"
+          end
         when :string, :str
           info_values.call(LibHTS::BCF_HT_STR)
-                     .read_pointer.read_string
+                     .read_string
+        end
+      end
+
+      def fields
+        n_info = @record.struct[:n_info]
+        Array.new(n_info) do |i|
+          fld = LibHTS::BcfInfo.new(
+            @record.struct[:d][:info] +
+            i * LibHTS::BcfInfo.size
+          )
+          {
+            name: LibHTS.bcf_hdr_int2id(
+              @record.bcf.header.struct, LibHTS::BCF_DT_ID, fld[:key]
+            ),
+            n: LibHTS.bcf_hdr_id2number(
+              @record.bcf.header.struct, LibHTS::BCF_HL_INFO, fld[:key]
+            ),
+            vtype: fld[:type], i: fld[:key]
+          }
+        end
+      end
+
+      private
+
+      def get_info_type(key)
+        @record.struct[:n_info].times do |i|
+          fld = LibHTS::BcfInfo.new(
+            @record.struct[:d][:info] +
+            i * LibHTS::BcfInfo.size
+          )
+          id = LibHTS.bcf_hdr_int2id(
+            @record.bcf.header.struct, LibHTS::BCF_DT_ID, fld[:key]
+          )
+          return fld[:type] if id == key
+        end
+      end
+
+      def info_type_to_string(t)
+        case t
+        when 0 then :flag
+        when 1, 2, 3, 4 then :int
+        when 5 then :float
+        when 7 then :string
+        else
+          raise "Unknown info type: #{t}"
         end
       end
     end

data/lib/hts/bcf/record.rb

@@ -29,12 +29,7 @@ module HTS
         hdr = @bcf.header.struct
         rid = @bcf1[:rid]
 
-        return nil if hdr.null? || rid < 0 || rid >= hdr[:n][LibHTS::BCF_DT_CTG]
-
-        LibHTS::BcfIdpair.new(
-          hdr[:id][LibHTS::BCF_DT_CTG].to_ptr +
-          LibHTS::BcfIdpair.size * rid # offset
-        )[:key]
+        LibHTS.bcf_hdr_id2name(hdr, rid)
       end
 
       def pos
@@ -106,9 +101,8 @@ module HTS
 
       def to_s
         ksr = LibHTS::KString.new
-        if LibHTS.vcf_format(@bcf.header.struct, @bcf1, ksr) == -1
-          raise "Failed to format record"
-        end
+        raise "Failed to format record" if LibHTS.vcf_format(@bcf.header.struct, @bcf1, ksr) == -1
+
         ksr[:s]
       end
     end

data/lib/hts/bcf.rb

@@ -4,15 +4,13 @@
 # https://github.com/quinlan-lab/hts-python
 
 require_relative "bcf/header"
-require_relative "bcf/record"
 require_relative "bcf/info"
 require_relative "bcf/format"
-require_relative "utils/open_method"
+require_relative "bcf/record"
 
 module HTS
   class Bcf
     include Enumerable
-    extend Utils::OpenMethod
 
     attr_reader :file_path, :mode, :header
     # HtfFile is FFI::BitStruct
@@ -35,9 +33,6 @@ module HTS
       @htf_file  = LibHTS.hts_open(file_path, mode)
       @header    = Bcf::Header.new(LibHTS.bcf_hdr_read(htf_file))
 
-      # FIXME: should be defined here?
-      @bcf1      = LibHTS.bcf_init
-
       # IO like API
       if block_given?
         begin
@@ -61,11 +56,14 @@ module HTS
       LibHTS.hts_close(htf_file)
     end
 
-    def each(&block)
-      while LibHTS.bcf_read(htf_file, header, @bcf1) != -1
-        record = Record.new(@bcf1, self)
-        block.call(record)
+    def each
+      return to_enum(__method__) unless block_given?
+
+      while LibHTS.bcf_read(htf_file, header, bcf1 = LibHTS.bcf_init) != -1
+        record = Record.new(bcf1, self)
+        yield record
       end
+      self
     end
 
     def n_samples

data/lib/hts/faidx.rb

@@ -3,17 +3,26 @@
 # Based on hts-python
 # https://github.com/quinlan-lab/hts-python
 
-require_relative "utils/open_method"
-
 module HTS
   class Faidx
-    extend Utils::OpenMethod
-
     attr_reader :file_path
 
+    class << self
+      alias open new
+    end
+
     def initialize(file_path)
       @file_path = File.expand_path(file_path)
       @fai = LibHTS.fai_load(file_path)
+
+      # IO like API
+      if block_given?
+        begin
+          yield self
+        ensure
+          close
+        end
+      end
     end
 
     def close

data/lib/hts/ffi_ext/struct.rb

@@ -1,6 +1,6 @@
 # frozen_string_literal: true
 
-require "ffi/bit_struct"
+require 'ffi/bit_field'
 
 module FFI
   class Struct

data/lib/hts/libhts/constants.rb

@@ -289,7 +289,7 @@ module HTS
         :isize,          :hts_pos_t
     end
 
-    class Bam1 < FFI::Struct
+    class Bam1 < FFI::ManagedStruct
       layout \
         :core,           Bam1Core,
         :id,             :uint64,
@@ -301,6 +301,10 @@ module HTS
       # bit_fields :_mempolicy,
       #            :mempolicy,  2,
       #            :_reserved,  30
+
+      def self.release(ptr)
+        LibHTS.bam_destroy1(ptr) unless ptr.null?
+      end
     end
 
     typedef :pointer, :bam_plp
@@ -457,7 +461,7 @@ module HTS
         :id,             :string,
         :als,            :pointer, # (\\0-separated string)
         :allele,         :pointer,
-        :info,           BcfInfo.ptr,
+        :info,           :pointer, # BcfInfo.ptr,
         :fmt,            BcfFmt.ptr,
         :var,            BcfVariant.ptr,
         :n_var,          :int,
@@ -466,7 +470,7 @@ module HTS
         :indiv_dirty,    :int
     end
 
-    class Bcf1 < FFI::BitStruct
+    class Bcf1 < FFI::ManagedBitStruct
       layout \
         :pos,            :hts_pos_t,
         :rlen,           :hts_pos_t,
@@ -489,6 +493,10 @@ module HTS
       bit_fields :_n_fmt_sample,
                  :n_fmt,    8,
                  :n_sample, 24
+
+      def self.release(ptr)
+        LibHTS.bcf_destroy(ptr) unless ptr.null?
+      end
     end
   end
 end

data/lib/hts/libhts/vcf.rb

@@ -167,6 +167,33 @@ module HTS
           LibHTS::BcfIdpair.size * int_id # offsets
         )[:key]
       end
+
+      def bcf_hdr_name2id(hdr, id)
+        bcf_hdr_id2int(hdr, BCF_DT_CTG, id)
+      end
+
+      def bcf_hdr_id2name(hdr, rid)
+        return nil if hdr.null? || rid < 0 || rid >= hdr[:n][LibHTS::BCF_DT_CTG]
+
+        LibHTS::BcfIdpair.new(
+          hdr[:id][LibHTS::BCF_DT_CTG].to_ptr +
+          LibHTS::BcfIdpair.size * rid # offset
+        )[:key]
+      end
+
+      def bcf_hdr_id2length(hdr, type, int_id)
+        LibHTS::BcfIdpair.new(
+          hdr[:id][LibHTS::BCF_DT_ID].to_ptr +
+          LibHTS::BcfIdpair.size * int_id # offset
+        )[:val][:info][type] >> 8 & 0xf
+      end
+
+      def bcf_hdr_id2number(hdr, type, int_id)
+        LibHTS::BcfIdpair.new(
+          hdr[:id][LibHTS::BCF_DT_ID].to_ptr +
+          LibHTS::BcfIdpair.size * int_id # offset
+        )[:val][:info][type] >> 12
+      end
     end
 
     # constants

data/lib/hts/tabix.rb

@@ -3,13 +3,21 @@
 # Based on hts-python
 # https://github.com/quinlan-lab/hts-python
 
-require_relative "utils/open_method"
-
 module HTS
   class Tabix
-    extend Utils::OpenMethod
-
-    def initialize; end
+    class << self
+      alias open new
+    end
+    def initialize
+      # IO like API
+      if block_given?
+        begin
+          yield self
+        ensure
+          close
+        end
+      end
+    end
 
     def build; end
 

data/lib/hts/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module HTS
-  VERSION = "0.0.4"
+  VERSION = "0.0.5"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: htslib
 version: !ruby/object:Gem::Version
-  version: 0.0.4
+  version: 0.0.5
 platform: ruby
 authors:
 - kojix2
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-12-22 00:00:00.000000000 Z
+date: 2021-12-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -155,7 +155,6 @@ files:
 - lib/hts/libhts/tbx.rb
 - lib/hts/libhts/vcf.rb
 - lib/hts/tabix.rb
-- lib/hts/utils/open_method.rb
 - lib/hts/version.rb
 - lib/htslib.rb
 homepage: https://github.com/kojix2/ruby-htslib
@@ -177,7 +176,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.2.26
+rubygems_version: 3.3.3
 signing_key: 
 specification_version: 4
 summary: HTSlib bindings for Ruby

data/lib/hts/utils/open_method.rb

@@ -1,17 +0,0 @@
-# frozen_string_literal: true
-
-module HTS
-  module Utils
-    module OpenMethod
-      def open(path)
-        object = new(path)
-        if block_given?
-          yield(object)
-          object.close
-        else
-          object
-        end
-      end
-    end
-  end
-end