htslib 0.2.6 → 0.2.8

checksums.yaml

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data/README.md

@@ -17,7 +17,7 @@ Ruby-htslib is the [Ruby](https://www.ruby-lang.org) bindings to [HTSlib](https:
   - Ubuntu : `apt install libhts-dev`
   - macOS : `brew install htslib`
   - Windows : [mingw-w64-htslib](https://packages.msys2.org/base/mingw-w64-htslib) is automatically fetched when installing the gem ([RubyInstaller](https://rubyinstaller.org) only).
-  - Build from source code (see Development section)
+  - Build from source code (see the Development section)
 
 ## Installation
 
@@ -30,10 +30,10 @@ will automatically detect the location of the shared library. If pkg-config does
 Alternatively, you can specify the directory of the shared library by setting the environment variable `HTSLIBDIR`.
 
 ```sh
-export HTSLIBDIR="/your/path/to/htslib" # libhts.so
+export HTSLIBDIR="/your/path/to/htslib" # Directory where libhts.so is located
 ```
 
-ruby-htslib also works on Windows; if you use RubyInstaller, htslib will be prepared automatically.
+ruby-htslib also works on Windows. If you use RubyInstaller, htslib will be prepared automatically.
 
 ## Usage
 
@@ -64,12 +64,24 @@ end
 bam.close
 ```
 
+With a block
+
+```ruby
+HTS::Bam.open("test/fixtures/moo.bam") do |bam|
+  bam.each do |r|
+    puts r.to_s
+  end
+end
+```
+
 ### HTS::Bcf - VCF / BCF - Variant Call Format file
 
 Reading fields
 
 ```ruby
-bcf = HTS::Bcf.open("b.bcf")
+require 'htslib'
+
+bcf = HTS::Bcf.open("test/fixtures/test.bcf")
 
 bcf.each do |r|
   p chrom:  r.chrom,
@@ -86,27 +98,38 @@ end
 bcf.close
 ```
 
+With a block
+
+```ruby
+HTS::Bcf.open("test/fixtures/test.bcf") do |bcf|
+  bcf.each do |r|
+    puts r.to_s
+  end
+end
+```
+
 ### HTS::Faidx - FASTA / FASTQ - Nucleic acid sequence
 
 ```ruby
-fa = HTS::Faidx.open("c.fa")
-fa.seq("chr1:1-10")
+fa = HTS::Faidx.open("test/fixtures/moo.fa")
+fa.seq("chr1:1-10") # => CGCAACCCGA # 1-based
+fa.close
 ```
 
-### HTS::Tbx - Tabix - gff, bed, sam, vcf
+### HTS::Tabix - GFF / BED - TAB-delimited genome position file
 
 ```ruby
-tb = HTS::Tbx.open("test.vcf.gz")
-tb.query("chr1", 10000, 20000) do |line|
-  p line
+tb = HTS::Tabix.open("test/fixtures/test.vcf.gz")
+tb.query("poo", 2000, 3000) do |line|
+  puts line.join("\t")
 end
+tb.close
 ```
 
-Note: Faidx or Tbx should not be explicitly closed. See [#27](https://github.com/kojix2/ruby-htslib/issues/27)
-
 ### Low-level API
 
-`HTS::LibHTS` provides native C functions.
+Middle architectural layer between high-level Ruby code and low-level C code.
+`HTS::LibHTS` provides native C functions using [Ruby-FFI](https://github.com/ffi/ffi). 
 
 ```ruby
 require 'htslib'
@@ -117,26 +140,31 @@ p b[:category]
 p b[:format]
 ```
 
-Macro functions
+The low-level API makes it possible to perform detailed operations, such as calling CRAM-specific functions.
 
-htslib has a lot of macro functions for speed. Ruby-FFI cannot call C macro functions. However, essential functions are reimplemented in Ruby, and you can call them.
+#### Macro functions
 
-Structs
+HTSlib is designed to improve performance with many macro functions. However, it is not possible to call C macro functions directly from Ruby-FFI. To overcome this, important macro functions have been re-implemented in Ruby, allowing them to be called in the same way as native functions.
 
-Only a small number of C structs are implemented with FFI's ManagedStruct, which frees memory when Ruby's garbage collection fires. Other structs will need to be freed manually.
+#### Garbage Collection and Memory Freeing
+
+A small number of commonly used structs, such as `Bam1` and `Bcf1`, are implemented using FFI's `ManagedStruct`. This allows for automatic memory release when Ruby's garbage collection is triggered. On the other hand, other structs are implemented using `FFI::Struct`, and they will require manual memory release.
 
 ### Need more speed?
 
-Try Crystal. [HTS.cr](https://github.com/bio-cr/hts.cr) is implemented in Crystal language and provides an API compatible with ruby-htslib. Crystal language is not as flexible as Ruby language. You can not use `eval` methods and must always be careful with the types. Writing one-time scripts in Crystal may be less fun. However, if you have a clear idea of what you want to do in your mind, have already written code in Ruby, and need to run them over and over, try creating a command line tool in Crystal. The Crystal language is as fast as the Rust and C languages. It will give you incredible power to make tools.
+Try Crystal. [HTS.cr](https://github.com/bio-cr/hts.cr) is implemented in Crystal language and provides an API compatible with ruby-htslib. 
 
 ## Documentation
 
 - [TUTORIAL.md](TUTORIAL.md)
 - [API Documentation (develop branch)](https://kojix2.github.io/ruby-htslib/)
-- [RubyDoc.info - HTSlib](https://rdoc.info/gems/htslib)
+- [API Documentation (released gem)](https://rubydoc.info/gems/htslib)
 
 ## Development
 
+#### Compile from source code
+
+[GNU Autotools](https://en.wikipedia.org/wiki/GNU_Autotools) is required to compile htslib.
 To get started with development:
 
 ```sh
@@ -147,21 +175,41 @@ bundle exec rake htslib:build
 bundle exec rake test
 ```
 
-[GNU Autotools](https://en.wikipedia.org/wiki/GNU_Autotools) is required to compile htslib.
+#### Macro functions are reimplemented
 
 HTSlib has many macro functions. These macro functions cannot be called from FFI and must be reimplemented in Ruby.
 
-- Use the new version of Ruby to take full advantage of Ruby's potential.
-  - This is possible because we have a small number of users.
-- Remain compatible with [HTS.cr](https://github.com/bio-cr/hts.cr).
-  - The most challenging part is the return value. In the Crystal language, methods are expected to return only one type. On the other hand, in the Ruby language, methods that return multiple classes are very common. For example, in the Crystal language, the compiler gets confused if the return value is one of six types: Int32, Int64, Float32, Float64, Nil, or String. In fact Crystal allows you to do that. But the code gets a little messy. In Ruby, this is very common and doesn't cause any problems.
-  - Ruby and Crystal are languages that use garbage collection. However, the memory release policy for allocated C structures is slightly different: in Ruby-FFI, you can define a `self.release` method in `FFI::Struct`. This method is called when GC. So you don't have to worry about memory in high-level APIs like Bam::Record or Bcf::Record, etc. Crystal requires you to define a finalize method on each class. So you need to define it in Bam::Record or Bcf::Record.
+#### Use the latest Ruby
+
+Use Ruby 3 or newer to take advantage of new features. This is possible because we have a small number of users.
+
+#### Keep compatibility with Crystal language
+
+Compatibility with Crystal language is important for Ruby-htslib development. 
+
+- [HTS.cr](https://github.com/bio-cr/hts.cr) - HTSlib bindings for Crystal
+
+Return value
+
+The most challenging part is the return value. In the Crystal language, methods are expected to return only one type. On the other hand, in the Ruby language, methods that return multiple classes are very common. For example, in the Crystal language, the compiler gets confused if the return value is one of six types: Int32, Int64, Float32, Float64, Nil, or String. In fact Crystal allows you to do that. But the code gets a little messy. In Ruby, this is very common and doesn't cause any problems.
+
+Memory management
+
+Ruby and Crystal are languages that use garbage collection. However, the memory release policy for allocated C structures is slightly different: in Ruby-FFI, you can define a `self.release` method in `FFI::Struct`. This method is called when GC. So you don't have to worry about memory in high-level APIs like Bam::Record or Bcf::Record, etc. Crystal requires you to define a finalize method on each class. So you need to define it in Bam::Record or Bcf::Record.
+
+Macro functions
+
+In ruby-htslib, C macro functions are added to `LibHTS`, but in Crystal, `LibHTS` is a Lib, so methods cannot be added. methods are added to `LibHTS2`.
+
+#### Naming convention
+
+If you are not sure about the naming of a method, follow the Rust-htslib API. This is a very weak rule. if a more appropriate name is found later in Ruby, it will replace it.
 
-Method naming generally follows the Rust-htslib API.
+#### Support for bitfields of structures
 
-#### FFI Extensions
+Since Ruby-FFI does not support structure bit fields, the following extensions are used.
 
-- [ffi-bitfield](https://github.com/kojix2/ffi-bitfield) : Extension of Ruby-FFI to support bitfields.
+- [ffi-bitfield](https://github.com/kojix2/ffi-bitfield) - Extension of Ruby-FFI to support bitfields.
 
 #### Automatic validation
 
@@ -180,7 +228,7 @@ Ruby-htslib is a library under development, so even minor improvements like typo
 - [financial contributions](https://github.com/sponsors/kojix2)
 
 ```markdown
-# Ownership and Commitment Rights
+# Ownership and Commit Rights
 
 Do you need commit rights to the ruby-htslib repository?
 Do you want to get admin rights and take over the project?

data/TUTORIAL.md

@@ -38,7 +38,7 @@ class Bcf{
   +each() Enumerable
   +query()
 }
-class Tbx~Hts~{
+class Tabix~Hts~{
   +@hts_file : FFI::Struct
 }
 class `Bam::Header`{
@@ -46,32 +46,46 @@ class `Bam::Header`{
   +struct()
   +target_count()
   +target_names()
+  +name2tid()
+  +tid2name()
   +to_s()
 }
 class `Bam::Record` {
   +@bam1 : FFI::Struct
   +@header : Bam::Header
   +struct()
+  +qname()
+  +qname=()
   +tid()
   +tid=()
   +mtid()
   +mtid=()
   +pos()
   +pos=()
-  +mpos()
-  +mpos=()
+  +mpos() +mate_pos()
+  +mpos=() +mate_pos=()
   +bin()
   +bin=()
-  +qname()
-  +flag()
-  +chorm()
+  +endpos()
+  +chorm() +contig()
+  +mate_chrom() +mate_contig()
+  +strand()
+  +mate_strand()
+  +isize() +insert_size()
+  +isize=() +insert_size=()
   +mapq()
+  +mapq=()
   +cigar()
-  +mate_chrom()
-  +isize()
-  +seq()
+  +qlen()
+  +rlen()
+  +seq() +sequence()
+  +len()
+  +base(n)
   +qual()
   +qual_string()
+  +base_qual(n)
+  +flag()
+  +flag=()
   +aux()
   +to_s()
 }
@@ -91,12 +105,19 @@ class `Bcf::Record`{
   +@bcf1 : FFI::Struct
   +@header : Bcf::Header
   +struct()
+  +rid()
+  +rid=()
   +chrom()
   +pos()
+  +pos=()
   +id()
-  +qual()
+  +id=()
+  +clear_id()
   +ref()
   +alt()
+  +alleles()
+  +qual()
+  +qual=()
   +filter()
   +info()
   +format()
@@ -164,6 +185,20 @@ class Faidx{
 
 ```
 
+## Installation
+
+```
+gem install htslib
+```
+
+You can check which shared libraries are used by ruby-htslib as follows
+
+```ruby
+require "htslib"
+puts HTS.lib_path
+# => "/home/kojix2/.rbenv/versions/3.2.0/lib/ruby/gems/3.2.0/gems/htslib-0.2.6/vendor/libhts.so"
+```
+
 ## HTS::Bam - SAM / BAM / CRAM - Sequence Alignment Map file
 
 Reading fields
@@ -194,9 +229,8 @@ bam.close
 Open with block
 
 ```ruby
-HTS::Bam.open("test/fixtures/moo.bam") do |b|
-  b.
-  do |r|
+HTS::Bam.open("test/fixtures/moo.bam") do |bam|
+  bam.each do |record|
     # ...
   end
 end
@@ -220,6 +254,18 @@ in.close
 out.close
 ```
 
+Create index
+
+```ruby
+HTS::Bam.open("foo.bam", build_index: true)
+```
+
+```
+b = HTS::Bam.open("foo.bam")
+            .build_index
+            .load_index
+```
+
 ## HTS::Bcf - VCF / BCF - Variant Call Format file
 
 Reading fields
@@ -245,8 +291,8 @@ bcf.close
 Open with block
 
 ```ruby
-HTS::Bcf.open("b.bcf") do |b|
-  b.each do |r|
+HTS::Bcf.open("b.bcf") do |bcf|
+  bcf.each do |record|
     # ...
   end
 end

data/lib/hts/bam/auxi.rb

@@ -3,8 +3,11 @@
 # Q. Why is the file name auxi.rb and not aux.rb?
 #
 # A. This is for compatibility with Windows.
+#
 # In Windows, aux is a reserved word
-# You cannot create a file named aux. Eww!
+# You cannot create a file named aux.
+#
+# What?! That's crazy!
 
 module HTS
   class Bam < Hts
@@ -15,6 +18,7 @@ module HTS
     # Ruby's Aux class references a part of it. There is no one-to-one
     # correspondence between C structures and Ruby's Aux class.
     class Aux
+      include Enumerable
       attr_reader :record
 
       def initialize(record)
@@ -29,24 +33,7 @@ module HTS
         aux = LibHTS.bam_aux_get(@record.struct, key)
         return nil if aux.null?
 
-        type = type ? type.to_s : aux.read_string(1)
-
-        # A (character), B (general array),
-        # f (real number), H (hexadecimal array),
-        # i (integer), or Z (string).
-
-        case type
-        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" # char
-          LibHTS.bam_aux2A(aux).chr
-        else
-          raise NotImplementedError, "type: #{t}"
-        end
+        get_ruby_aux(aux, type)
       end
 
       # For compatibility with HTS.cr.
@@ -67,6 +54,76 @@ module HTS
       def [](key)
         get(key)
       end
+
+      def first
+        aux = LibHTS.bam_aux_first(@record.struct)
+        return nil if aux.null?
+
+        get_ruby_aux(aux)
+      end
+
+      def each
+        return enum_for(__method__) unless block_given?
+
+        aux = LibHTS.bam_aux_first(@record.struct)
+        return nil if aux.null?
+
+        loop do
+          yield get_ruby_aux(aux)
+          aux = LibHTS.bam_aux_next(@record.struct, aux)
+          break if aux.null?
+        end
+      end
+
+      def to_h
+        h = {}
+        aux = LibHTS.bam_aux_first(@record.struct)
+        return h if aux.null?
+
+        loop do
+          key = FFI::Pointer.new(aux.address - 2).read_string(2)
+          h[key] = get_ruby_aux(aux)
+          aux = LibHTS.bam_aux_next(@record.struct, aux)
+          break if aux.null?
+        end
+        h
+      end
+
+      private
+
+      def get_ruby_aux(aux, type = nil)
+        type = type ? type.to_s : aux.read_string(1)
+
+        # A (character), B (general array),
+        # f (real number), H (hexadecimal array),
+        # i (integer), or Z (string).
+
+        case type
+        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" # char
+          LibHTS.bam_aux2A(aux).chr
+        when "B" # array
+          t2 = aux.read_string(2)[1] # just a little less efficient
+          l = LibHTS.bam_auxB_len(aux)
+          case t2
+          when "c", "C", "s", "S", "i", "I"
+            # FIXME : Not efficient.
+            Array.new(l) { |i| LibHTS.bam_auxB2i(aux, i) }
+          when "f", "d"
+            # FIXME : Not efficient.
+            Array.new(l) { |i| LibHTS.bam_auxB2f(aux, i) }
+          else
+            raise NotImplementedError, "type: #{type} #{t2}"
+          end
+        else
+          raise NotImplementedError, "type: #{type}"
+        end
+      end
     end
   end
 end

data/lib/hts/bam/header.rb

@@ -87,6 +87,14 @@ module HTS
         LibHTS.sam_hdr_str(@sam_hdr)
       end
 
+      def name2tid(name)
+        LibHTS.sam_hdr_name2tid(@sam_hdr, name)
+      end
+
+      def tid2name(tid)
+        LibHTS.sam_hdr_tid2name(@sam_hdr, tid)
+      end
+
       private
 
       def initialize_copy(orig)

data/lib/hts/bam/record.rb

@@ -12,8 +12,8 @@ module HTS
 
       attr_reader :header
 
-      def initialize(bam1_t, header)
-        @bam1 = bam1_t
+      def initialize(header, bam1_t = nil)
+        @bam1 = bam1_t || LibHTS.bam_init1
         @header = header
       end
 
@@ -32,6 +32,10 @@ module HTS
         LibHTS.bam_get_qname(@bam1).read_string
       end
 
+      def qname=(name)
+        LibHTS.bam_set_qname(@bam1, name)
+      end
+
       # Get the chromosome ID of the alignment. -1 if not mapped.
       # @return [Integer] chromosome ID
       def tid
@@ -178,7 +182,7 @@ module HTS
       def seq
         r = LibHTS.bam_get_seq(@bam1)
         seq = String.new
-        (@bam1[:core][:l_qseq]).times do |i|
+        len.times do |i|
           seq << SEQ_NT16_STR[LibHTS.bam_seqi(r, i)]
         end
         seq
@@ -195,8 +199,8 @@ module HTS
       # @param [Integer] i index
       # @return [String] base
       def base(n)
-        n += @bam1[:core][:l_qseq] if n < 0
-        return "." if (n >= @bam1[:core][:l_qseq]) || (n < 0) # eg. base(-1000)
+        n += len if n < 0
+        return "." if (n >= len) || (n < 0) # eg. base(-1000)
 
         r = LibHTS.bam_get_seq(@bam1)
         SEQ_NT16_STR[LibHTS.bam_seqi(r, n)]
@@ -206,7 +210,7 @@ module HTS
       # @return [Array] base qualities
       def qual
         q_ptr = LibHTS.bam_get_qual(@bam1)
-        q_ptr.read_array_of_uint8(@bam1[:core][:l_qseq])
+        q_ptr.read_array_of_uint8(len)
       end
 
       # Get the base qualities as a string. (a.k.a QUAL)
@@ -220,8 +224,8 @@ module HTS
       # @param [Integer] i index
       # @return [Integer] base quality
       def base_qual(n)
-        n += @bam1[:core][:l_qseq] if n < 0
-        return 0 if (n >= @bam1[:core][:l_qseq]) || (n < 0) # eg. base_qual(-1000)
+        n += len if n < 0
+        return 0 if (n >= len) || (n < 0) # eg. base_qual(-1000)
 
         q_ptr = LibHTS.bam_get_qual(@bam1)
         q_ptr.get_uint8(n)
@@ -256,11 +260,11 @@ module HTS
         end
       end
 
-      # TODO: add a method to get the auxillary fields as a hash.
+      # TODO: add a method to get the auxiliary fields as a hash.
 
-      # TODO: add a method to set the auxillary fields.
+      # TODO: add a method to set the auxiliary fields.
 
-      # TODO: add a method to remove the auxillary fields.
+      # TODO: add a method to remove the auxiliary fields.
 
       # TODO: add a method to set variable length data (qname, cigar, seq, qual).
 

data/lib/hts/bam.rb

@@ -114,29 +114,12 @@ module HTS
     def write(record)
       check_closed
 
-      # record = record.dup
       r = LibHTS.sam_write1(@hts_file, header, record)
       raise "Failed to write record" if r < 0
     end
 
-    def <<(aln)
-      write(aln)
-    end
-
-    def each(copy: false, &block)
-      if copy
-        each_record_copy(&block)
-      else
-        each_record_reuse(&block)
-      end
-    end
-
-    def query(region, copy: false, &block)
-      if copy
-        query_copy(region, &block)
-      else
-        query_reuse(region, &block)
-      end
+    def <<(record)
+      write(record)
     end
 
     # @!macro [attach] define_getter
@@ -158,9 +141,10 @@ module HTS
     alias isize insert_size
     alias mpos mate_pos
 
+    # FXIME: experimental
     def aux(tag)
-      warn "experimental"
       check_closed
+
       position = tell
       ary = map { |r| r.aux(tag) }
       seek(position)
@@ -185,8 +169,8 @@ module HTS
     alias each_isize each_insert_size
     alias each_mpos each_mate_pos
 
+    # FIXME: experimental
     def each_aux(tag)
-      warn "experimental"
       check_closed
       return to_enum(__method__, tag) unless block_given?
 
@@ -197,47 +181,44 @@ module HTS
       self
     end
 
-    private
+    def each(copy: false, &block)
+      if copy
+        each_record_copy(&block)
+      else
+        each_record_reuse(&block)
+      end
+    end
 
-    def query_reuse(region)
+    def query(region, beg = nil, end_ = nil, copy: false, &block)
       check_closed
       raise "Index file is required to call the query method." unless index_loaded?
-      return to_enum(__method__, region) unless block_given?
-
-      qiter = LibHTS.sam_itr_querys(@idx, header, region)
-      raise "Failed to query region: #{region}" if qiter.null?
 
-      bam1 = LibHTS.bam_init1
-      record = Record.new(bam1, header)
-      begin
-        yield record while LibHTS.sam_itr_next(@hts_file, qiter, bam1) > 0
-      ensure
-        LibHTS.hts_itr_destroy(qiter)
+      if beg && end_
+        tid = header.name2tid(region)
+        queryi(tid, beg, end_, copy:, &block)
+      elsif beg.nil? && end_.nil?
+        querys(region, copy:, &block)
+      else
+        raise ArgumentError, "beg and end_ must be specified together"
       end
-      self
     end
 
-    def query_copy(region)
-      check_closed
-      raise "Index file is required to call the query method." unless index_loaded?
-      return to_enum(__method__, region) unless block_given?
+    private
 
-      qiter = LibHTS.sam_itr_querys(@idx, header, region)
-      raise "Failed to query region: #{region}" if qiter.null?
+    def queryi(tid, beg, end_, copy: false, &block)
+      if copy
+        queryi_copy(tid, beg, end_, &block)
+      else
+        queryi_reuse(tid, beg, end_, &block)
+      end
+    end
 
-      begin
-        loop do
-          bam1 = LibHTS.bam_init1
-          slen = LibHTS.sam_itr_next(@hts_file, qiter, bam1)
-          break if slen == -1
-          raise if slen < -1
-
-          yield Record.new(bam1, header)
-        end
-      ensure
-        LibHTS.hts_itr_destroy(qiter)
+    def querys(region, copy: false, &block)
+      if copy
+        querys_copy(region, &block)
+      else
+        querys_reuse(region, &block)
       end
-      self
     end
 
     def each_record_reuse
@@ -247,7 +228,7 @@ module HTS
       return to_enum(__method__) unless block_given?
 
       bam1 = LibHTS.bam_init1
-      record = Record.new(bam1, header)
+      record = Record.new(header, bam1)
       yield record while LibHTS.sam_read1(@hts_file, header, bam1) != -1
       self
     end
@@ -257,10 +238,73 @@ module HTS
       return to_enum(__method__) unless block_given?
 
       while LibHTS.sam_read1(@hts_file, header, bam1 = LibHTS.bam_init1) != -1
-        record = Record.new(bam1, header)
+        record = Record.new(header, bam1)
         yield record
       end
       self
     end
+
+    def queryi_reuse(tid, beg, end_, &block)
+      return to_enum(__method__, region, beg, end_) unless block_given?
+
+      qiter = LibHTS.sam_itr_queryi(@idx, tid, beg, end_)
+      raise "Failed to query region: #{tid} #{beg} #{end_}" if qiter.null?
+
+      query_reuse_yield(qiter, &block)
+      self
+    end
+
+    def queryi_copy(tid, beg, end_, &block)
+      return to_enum(__method__, tid, beg, end_) unless block_given?
+
+      qiter = LibHTS.sam_itr_queryi(@idx, tid, beg, end_)
+      raise "Failed to query region: #{tid} #{beg} #{end_}" if qiter.null?
+
+      query_copy(qiter, &block)
+      self
+    end
+
+    def querys_reuse(region, &block)
+      return to_enum(__method__, region) unless block_given?
+
+      qiter = LibHTS.sam_itr_querys(@idx, header, region)
+      raise "Failed to query region: #{region}" if qiter.null?
+
+      query_reuse_yield(qiter, &block)
+      self
+    end
+
+    def querys_copy(region, &block)
+      return to_enum(__method__, region) unless block_given?
+
+      qiter = LibHTS.sam_itr_querys(@idx, header, region)
+      raise "Failed to query region: #{region}" if qiter.null?
+
+      query_copy(qiter, &block)
+      self
+    end
+
+    def query_reuse_yield(qiter)
+      bam1 = LibHTS.bam_init1
+      record = Record.new(header, bam1)
+      begin
+        yield record while LibHTS.sam_itr_next(@hts_file, qiter, bam1) > 0
+      ensure
+        LibHTS.hts_itr_destroy(qiter)
+      end
+    end
+
+    def query_copy(qiter)
+      loop do
+        bam1 = LibHTS.bam_init1
+        slen = LibHTS.sam_itr_next(@hts_file, qiter, bam1)
+        break if slen == -1
+        raise if slen < -1
+
+        yield Record.new(header, bam1)
+      end
+    ensure
+      LibHTS.hts_itr_destroy(qiter)
+    end
   end
 end

data/lib/hts/bcf/header.rb

@@ -94,6 +94,14 @@ module HTS
         kstr[:s]
       end
 
+      def name2id(name)
+        LibHTS.bcf_hdr_name2id(@bcf_hdr, name)
+      end
+
+      def id2name(id)
+        LibHTS.bcf_hdr_id2name(@bcf_hdr, id)
+      end
+
       private
 
       def bcf_hl_type_to_int(bcf_hl_type)

data/lib/hts/bcf/record.rb

@@ -4,8 +4,8 @@ module HTS
   class Bcf < Hts
     # A class for working with VCF records.
     class Record
-      def initialize(bcf_t, header)
-        @bcf1 = bcf_t
+      def initialize(header, bcf_t = nil)
+        @bcf1 = bcf_t || LibHTS.bcf_init
         @header = header
       end
 

data/lib/hts/bcf.rb

@@ -63,7 +63,7 @@ module HTS
         warn "Create index for #{@file_name}"
       end
       case LibHTS.bcf_index_build3(@file_name, index_name, min_shift, (@nthreads || threads))
-      when 0 # sccessful
+      when 0 # successful
       when -1 then raise "indexing failed"
       when -2 then raise "opening #{@file_name} failed"
       when -3 then raise "format not indexable"
@@ -98,7 +98,7 @@ module HTS
     def write_header(header)
       check_closed
 
-      @header = header.dup
+      @header = header.clone
       LibHTS.bcf_hdr_write(@hts_file, header)
     end
 
@@ -130,35 +130,6 @@ module HTS
       header.samples
     end
 
-    def each(copy: false, &block)
-      if copy
-        each_record_copy(&block)
-      else
-        each_record_reuse(&block)
-      end
-    end
-
-    def query(...)
-      querys(...) # Fixme
-    end
-
-    # def queryi
-    # end
-
-    def querys(region, copy: false, &block)
-      if copy
-        querys_copy(region, &block)
-      else
-        querys_reuse(region, &block)
-      end
-    end
-
-    # private def queryi_copy
-    # end
-
-    # private def queryi_reuse
-    # end
-
     # @!macro [attach] define_getter
     #   @method $1
     #   Get $1 array
@@ -230,20 +201,71 @@ module HTS
       end
     end
 
-    private
+    def each(copy: false, &block)
+      if copy
+        each_record_copy(&block)
+      else
+        each_record_reuse(&block)
+      end
+    end
 
-    def querys_reuse(region)
+    def query(region, beg = nil, end_ = nil, copy: false, &block)
       check_closed
 
       raise "query is only available for BCF files" unless file_format == "bcf"
       raise "Index file is required to call the query method." unless index_loaded?
+
+      if beg && end_
+        tid = header.name2id(region)
+        queryi(tid, beg, end_, copy:, &block)
+      elsif beg.nil? && end_.nil?
+        querys(region, copy:, &block)
+      else
+        raise ArgumentError, "beg and end must be specified together"
+      end
+    end
+
+    private
+
+    def queryi(tid, beg, end_, copy: false, &block)
+      if copy
+        queryi_copy(tid, beg, end_, &block)
+      else
+        queryi_reuse(tid, beg, end_, &block)
+      end
+    end
+
+    def querys(region, copy: false, &block)
+      if copy
+        querys_copy(region, &block)
+      else
+        querys_reuse(region, &block)
+      end
+    end
+
+    def queryi_reuse(tid, beg, end_, &block)
+      return to_enum(__method__, tid, beg, end_) unless block_given?
+
+      qiter = LibHTS.bcf_itr_queryi(@idx, tid, beg, end_)
+      raise "Failed to query region #{tid} #{beg} #{end_}" if qiter.null?
+
+      query_reuse_yield(qiter, &block)
+      self
+    end
+
+    def querys_reuse(region, &block)
       return to_enum(__method__, region) unless block_given?
 
       qiter = LibHTS.bcf_itr_querys(@idx, header, region)
       raise "Failed to query region #{region}" if qiter.null?
 
+      query_reuse_yield(qiter, &block)
+      self
+    end
+
+    def query_reuse_yield(qiter)
       bcf1 = LibHTS.bcf_init
-      record = Record.new(bcf1, header)
+      record = Record.new(header, bcf1)
       begin
         loop do
           slen = LibHTS.hts_itr_next(@hts_file[:fp][:bgzf], qiter, bcf1, ::FFI::Pointer::NULL)
@@ -255,32 +277,39 @@ module HTS
       ensure
         LibHTS.bcf_itr_destroy(qiter)
       end
-      self
     end
 
-    def querys_copy(region)
-      check_closed
+    def queryi_copy(tid, beg, end_, &block)
+      return to_enum(__method__, tid, beg, end_) unless block_given?
 
-      raise "query is only available for BCF files" unless file_format == "bcf"
-      raise "Index file is required to call the query method." unless index_loaded?
+      qiter = LibHTS.bcf_itr_queryi(@idx, tid, beg, end_)
+      raise "Failed to query region #{tid} #{beg} #{end_}" if qiter.null?
+
+      query_copy_yield(qiter, &block)
+      self
+    end
+
+    def querys_copy(region, &block)
       return to_enum(__method__, region) unless block_given?
 
       qiter = LibHTS.bcf_itr_querys(@idx, header, region)
       raise "Failed to query region #{region}" if qiter.null?
 
-      begin
-        loop do
-          bcf1 = LibHTS.bcf_init
-          slen = LibHTS.hts_itr_next(@hts_file[:fp][:bgzf], qiter, bcf1, ::FFI::Pointer::NULL)
-          break if slen == -1
-          raise if slen < -1
+      query_copy_yield(qiter, &block)
+      self
+    end
 
-          yield Record.new(bcf1, header)
-        end
-      ensure
-        LibHTS.bcf_itr_destroy(qiter)
+    def query_copy_yield(qiter)
+      loop do
+        bcf1 = LibHTS.bcf_init
+        slen = LibHTS.hts_itr_next(@hts_file[:fp][:bgzf], qiter, bcf1, ::FFI::Pointer::NULL)
+        break if slen == -1
+        raise if slen < -1
+
+        yield Record.new(header, bcf1)
       end
-      self
+    ensure
+      LibHTS.bcf_itr_destroy(qiter)
     end
 
     def each_record_reuse
@@ -289,7 +318,7 @@ module HTS
       return to_enum(__method__) unless block_given?
 
       bcf1 = LibHTS.bcf_init
-      record = Record.new(bcf1, header)
+      record = Record.new(header, bcf1)
       yield record while LibHTS.bcf_read(@hts_file, header, bcf1) != -1
       self
     end
@@ -300,7 +329,7 @@ module HTS
       return to_enum(__method__) unless block_given?
 
       while LibHTS.bcf_read(@hts_file, header, bcf1 = LibHTS.bcf_init) != -1
-        record = Record.new(bcf1, header)
+        record = Record.new(header, bcf1)
         yield record
       end
       self

data/lib/hts/faidx/sequence.rb

@@ -1,5 +1,3 @@
-require_relative "../faidx"
-
 module HTS
   class Faidx
     class Sequence

data/lib/hts/faidx.rb

@@ -26,7 +26,8 @@ module HTS
       end
 
       @file_name = file_name
-      @fai = if [".fq", ".fastq"].include? File.extname(@file_name)
+      @fai = case File.extname(@file_name)
+             when ".fq", ".fastq"
                LibHTS.fai_load_format(@file_name, 2)
              else
                LibHTS.fai_load(@file_name)
@@ -40,7 +41,14 @@ module HTS
     end
 
     def close
+      return if closed?
+
       LibHTS.fai_destroy(@fai)
+      @fai = nil
+    end
+
+    def closed?
+      @fai.nil? || @fai.null?
     end
 
     def file_format
@@ -100,14 +108,14 @@ module HTS
       rlen = FFI::MemoryPointer.new(:int)
 
       if start.nil? && stop.nil?
-        result = LibHTS.fai_fetch(@fai, name, rlen)
+        result = LibHTS.fai_fetch64(@fai, name, rlen)
       else
         start < 0    && raise(ArgumentError, "Expect start to be >= 0")
         stop  < 0    && raise(ArgumentError, "Expect stop to be >= 0")
         start > stop && raise(ArgumentError, "Expect start to be <= stop")
         stop >= seq_len(name) && raise(ArgumentError, "Expect stop to be < seq_len")
 
-        result = LibHTS.faidx_fetch_seq(@fai, name, start, stop, rlen)
+        result = LibHTS.faidx_fetch_seq64(@fai, name, start, stop, rlen)
       end
 
       case rlen.read_int
@@ -125,14 +133,14 @@ module HTS
       rlen = FFI::MemoryPointer.new(:int)
 
       if start.nil? && stop.nil?
-        result = LibHTS.fai_fetchqual(@fai, name, rlen)
+        result = LibHTS.fai_fetchqual64(@fai, name, rlen)
       else
         start < 0    && raise(ArgumentError, "Expect start to be >= 0")
         stop  < 0    && raise(ArgumentError, "Expect stop to be >= 0")
         start > stop && raise(ArgumentError, "Expect start to be <= stop")
         stop >= seq_len(name) && raise(ArgumentError, "Expect stop to be < seq_len")
 
-        result = LibHTS.faidx_fetch_qual(@fai, name, start, stop, rlen)
+        result = LibHTS.faidx_fetch_qual64(@fai, name, start, stop, rlen)
       end
 
       case rlen.read_int

data/lib/hts/libhts/bgzf.rb

@@ -41,7 +41,7 @@ module HTS
       :ssize_t
 
     # Write _length_ bytes from _data_ to the file, the index will be used to
-    # decide the amount of uncompressed data to be writen to each bgzip block.
+    # decide the amount of uncompressed data to be written to each bgzip block.
     attach_function \
       :bgzf_block_write,
       [BGZF, :pointer, :size_t],

data/lib/hts/libhts/sam.rb

@@ -440,10 +440,22 @@ module HTS
       [SamHdr, Bam1, :pointer], # hts_filter_t
       :int
 
+    # Return a pointer to a BAM record's first aux field
+    attach_function \
+      :bam_aux_first,
+      [Bam1],
+      :pointer
+
+    # Return a pointer to a BAM record's next aux field
+    attach_function \
+      :bam_aux_next,
+      [Bam1, :pointer],
+      :pointer
+
     # Return a pointer to an aux record
     attach_function \
       :bam_aux_get,
-      [Bam1, :string], # FIXME
+      [Bam1, :string], # const char tag[2]
       :pointer
 
     # Get an integer aux value
@@ -570,17 +582,17 @@ module HTS
       [:bam_plp],
       :void
 
-    callback :bam_plp_callback_funcion, [:pointer, Bam1, BamPileupCd], :int
+    callback :bam_plp_callback_function, [:pointer, Bam1, BamPileupCd], :int
 
     # sets a callback to initialise any per-pileup1_t fields.
     attach_function \
       :bam_plp_constructor,
-      %i[bam_plp bam_plp_callback_funcion],
+      %i[bam_plp bam_plp_callback_function],
       :void
 
     attach_function \
       :bam_plp_destructor,
-      %i[bam_plp bam_plp_callback_funcion],
+      %i[bam_plp bam_plp_callback_function],
       :void
 
     # Get pileup padded insertion sequence
@@ -632,12 +644,12 @@ module HTS
 
     attach_function \
       :bam_mplp_constructor,
-      %i[bam_mplp bam_plp_callback_funcion],
+      %i[bam_mplp bam_plp_callback_function],
       :void
 
     attach_function \
       :bam_mplp_destructor,
-      %i[bam_mplp bam_plp_callback_funcion],
+      %i[bam_mplp bam_plp_callback_function],
       :void
 
     attach_function \

data/lib/hts/libhts.rb

@@ -37,5 +37,5 @@ require_relative "libhts/sam"
 require_relative "libhts/cram"
 require_relative "libhts/vcf"
 require_relative "libhts/tbx"
-require_relative "libhts/faidx"
+require_relative "libhts/fai"
 require_relative "libhts/thread_pool"

data/lib/hts/{tbx.rb → tabix.rb}

@@ -5,7 +5,7 @@ require_relative "../htslib"
 require_relative "hts"
 
 module HTS
-  class Tbx < Hts
+  class Tabix < Hts
     include Enumerable
 
     attr_reader :file_name, :index_name, :mode, :nthreads
@@ -22,9 +22,9 @@ module HTS
       file
     end
 
-    def initialize(file_name, mode = "r", index: nil, threads: nil, build_index: false)
+    def initialize(file_name, index: nil, threads: nil, build_index: false)
       if block_given?
-        message = "HTS::Tbx.new() dose not take block; Please use HTS::Tbx.open() instead"
+        message = "HTS::Tabix.new() dose not take block; Please use HTS::Tabix.open() instead"
         raise message
       end
 
@@ -32,17 +32,14 @@ module HTS
 
       @file_name  = file_name
       @index_name = index
-      @mode       = mode
+      @mode       = "r"
       @nthreads   = threads
-      @hts_file = LibHTS.hts_open(@file_name, @mode)
+      @hts_file   = LibHTS.hts_open(@file_name, @mode)
 
       raise Errno::ENOENT, "Failed to open #{@file_name}" if @hts_file.null?
 
       set_threads(threads) if threads
 
-      # return if @mode[0] == "w"
-      raise "Not implemented" if @mode[0] == "w"
-
       # build_index(index) if build_index
       @idx = load_index(index)
     end
@@ -63,7 +60,7 @@ module HTS
       !@idx.null?
     end
 
-    def tid(name)
+    def name2id(name)
       LibHTS.tbx_name2id(@idx, name)
     end
 
@@ -79,7 +76,7 @@ module HTS
       raise "Index file is required to call the query method." unless index_loaded?
 
       if start && end_
-        queryi(tid(region), start, end_, &block)
+        queryi(name2id(region), start, end_, &block)
       else
         querys(region, &block)
       end
@@ -87,36 +84,33 @@ module HTS
 
     private
 
-    def queryi(id, start, end_)
+    def queryi(id, start, end_, &block)
       return to_enum(__method__, id, start, end_) unless block_given?
 
       qiter = LibHTS.tbx_itr_queryi(@idx, id, start, end_)
-
       raise "Failed to query region: #{id}:#{start}-#{end_}" if qiter.null?
 
-      r = LibHTS::KString.new
-      begin
-        yield r[:s] while LibHTS.tbx_itr_next(@hts_file, @idx, qiter, r) > 0
-      ensure
-        LibHTS.hts_itr_destroy(qiter)
-      end
+      query_yield(qiter, &block)
       self
     end
 
-    def querys(region)
+    def querys(region, &block)
       return to_enum(__method__, region) unless block_given?
 
       qiter = LibHTS.tbx_itr_querys(@idx, region)
-
       raise "Failed to query region: #{region}" if qiter.null?
 
+      query_yield(qiter, &block)
+      self
+    end
+
+    def query_yield(qiter)
       r = LibHTS::KString.new
       begin
         yield r[:s].split("\t") while LibHTS.tbx_itr_next(@hts_file, @idx, qiter, r) > 0
       ensure
         LibHTS.hts_itr_destroy(qiter)
       end
-      self
     end
   end
 end

data/lib/hts/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module HTS
-  VERSION = "0.2.6"
+  VERSION = "0.2.8"
 end

data/lib/htslib.rb

@@ -55,6 +55,6 @@ module HTS
   autoload :Hts,    "hts/hts"
   autoload :Bam,    "hts/bam"
   autoload :Bcf,    "hts/bcf"
-  autoload :Tbx,    "hts/tbx"
   autoload :Faidx,  "hts/faidx"
+  autoload :Tabix,  "hts/tabix"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: htslib
 version: !ruby/object:Gem::Version
-  version: 0.2.6
+  version: 0.2.8
 platform: ruby
 authors:
 - kojix2
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2023-01-09 00:00:00.000000000 Z
+date: 2023-05-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -122,7 +122,7 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
-description: 
+description:
 email:
 - 2xijok@gmail.com
 executables: []
@@ -155,7 +155,7 @@ files:
 - lib/hts/libhts/bgzf.rb
 - lib/hts/libhts/constants.rb
 - lib/hts/libhts/cram.rb
-- lib/hts/libhts/faidx.rb
+- lib/hts/libhts/fai.rb
 - lib/hts/libhts/hfile.rb
 - lib/hts/libhts/hts.rb
 - lib/hts/libhts/kfunc.rb
@@ -166,7 +166,7 @@ files:
 - lib/hts/libhts/thread_pool.rb
 - lib/hts/libhts/vcf.rb
 - lib/hts/libhts/vcf_funcs.rb
-- lib/hts/tbx.rb
+- lib/hts/tabix.rb
 - lib/hts/version.rb
 - lib/htslib.rb
 homepage: https://github.com/kojix2/ruby-htslib
@@ -174,7 +174,7 @@ licenses:
 - MIT
 metadata:
   msys2_mingw_dependencies: htslib
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -189,8 +189,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.4.1
-signing_key: 
+rubygems_version: 3.4.10
+signing_key:
 specification_version: 4
 summary: HTSlib bindings for Ruby
 test_files: []