htslib 0.2.3 → 0.2.6

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data/README.md

@@ -8,17 +8,16 @@
 
 Ruby-htslib is the [Ruby](https://www.ruby-lang.org) bindings to [HTSlib](https://github.com/samtools/htslib), a C library for high-throughput sequencing data formats. It allows you to read and write file formats commonly used in genomics, such as [SAM, BAM, VCF, and BCF](http://samtools.github.io/hts-specs/), in the Ruby language.
 
-:apple: Feel free to fork it out if you can develop it! 
-
-:bowtie: Alpha stage.
+:apple: Feel free to fork it!
 
 ## Requirements
 
-* [Ruby](https://github.com/ruby/ruby) 3.1 or above.
-* [HTSlib](https://github.com/samtools/htslib)
-  * Ubuntu : `apt install libhts-dev`
-  * macOS : `brew install htslib`
-  * Build from source code (see Development section)
+- [Ruby](https://github.com/ruby/ruby) 3.1 or above.
+- [HTSlib](https://github.com/samtools/htslib)
+  - 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)
 
 ## Installation
 
@@ -26,7 +25,7 @@ Ruby-htslib is the [Ruby](https://www.ruby-lang.org) bindings to [HTSlib](https:
 gem install htslib
 ```
 
-If you have installed htslib with apt on Ubuntu or homebrew on Mac, [pkg-config](https://github.com/ruby-gnome/pkg-config) 
+If you have installed htslib with apt on Ubuntu or homebrew on Mac, [pkg-config](https://github.com/ruby-gnome/pkg-config)
 will automatically detect the location of the shared library. If pkg-config does not work well, set `PKG_CONFIG_PATH`.
 Alternatively, you can specify the directory of the shared library by setting the environment variable `HTSLIBDIR`.
 
@@ -34,11 +33,13 @@ Alternatively, you can specify the directory of the shared library by setting th
 export HTSLIBDIR="/your/path/to/htslib" # libhts.so
 ```
 
-## Overview
+ruby-htslib also works on Windows; if you use RubyInstaller, htslib will be prepared automatically.
+
+## Usage
 
-### High level API
+### HTS::Bam - SAM / BAM / CRAM - Sequence Alignment Map file
 
-Read SAM / BAM / CRAM - Sequence Alignment Map file
+Reading fields
 
 ```ruby
 require 'htslib'
@@ -56,14 +57,16 @@ bam.each do |r|
      mpos: r.mpos + 1,
      isiz: r.isize,
      seqs: r.seq,
-     qual: r.qual.map { |i| (i + 33).chr }.join,
+     qual: r.qual_string,
      MC:   r.aux("MC")
 end
 
 bam.close
 ```
 
-Read VCF / BCF - Variant Call Format file
+### HTS::Bcf - VCF / BCF - Variant Call Format file
+
+Reading fields
 
 ```ruby
 bcf = HTS::Bcf.open("b.bcf")
@@ -83,22 +86,27 @@ end
 bcf.close
 ```
 
-<details>
-<summary><b>Faidx</b></summary>
+### HTS::Faidx - FASTA / FASTQ - Nucleic acid sequence
 
 ```ruby
 fa = HTS::Faidx.open("c.fa")
+fa.seq("chr1:1-10")
+```
 
-fa.fetch("chr1:1-10")
+### HTS::Tbx - Tabix - gff, bed, sam, vcf
 
-fa.close
+```ruby
+tb = HTS::Tbx.open("test.vcf.gz")
+tb.query("chr1", 10000, 20000) do |line|
+  p line
+end
 ```
 
-</details>
+Note: Faidx or Tbx should not be explicitly closed. See [#27](https://github.com/kojix2/ruby-htslib/issues/27)
 
-### Low level API
+### Low-level API
 
-`HTS::LibHTS` provides native C functions. 
+`HTS::LibHTS` provides native C functions.
 
 ```ruby
 require 'htslib'
@@ -109,16 +117,23 @@ p b[:category]
 p b[:format]
 ```
 
-Note: htslib makes extensive use of macro functions for speed. You cannot use C macro functions in Ruby if they are not reimplemented in ruby-htslib. Only 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. 
+Macro 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.
+
+Structs
+
+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.
 
 ### Need more speed?
 
-Try Crystal. [htslib.cr](https://github.com/bio-crystal/htslib.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 you must always be careful with the data types. Writing one-time scripts in Crystal or playing with REPL may not be as much 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 fast, as fast as the Rust and C languages. It will give you great power to create 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. 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.
 
 ## Documentation
 
-* [API Documentation (develop branch)](https://kojix2.github.io/ruby-htslib/)
-* [RubyDoc.info - HTSlib](https://rdoc.info/gems/htslib)
+- [TUTORIAL.md](TUTORIAL.md)
+- [API Documentation (develop branch)](https://kojix2.github.io/ruby-htslib/)
+- [RubyDoc.info - HTSlib](https://rdoc.info/gems/htslib)
 
 ## Development
 
@@ -134,54 +149,57 @@ bundle exec rake test
 
 [GNU Autotools](https://en.wikipedia.org/wiki/GNU_Autotools) is required to compile htslib.
 
-Many macro functions are used in HTSlib. Since these macro functions cannot be called using FFI, they must be reimplemented in Ruby.
+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. What a deal!
-* Remain compatible with [htslib.cr](https://github.com/bio-crystal/htslib.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 can do this. But the code gets a little messy. In Ruby, this is very common and doesn't cause any problems. 
+- 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.
 
-In the script directory, there are several tools to help implement ruby-htslib. These tools may be forked into independent repository in the future.
+Method naming generally follows the Rust-htslib API.
 
 #### FFI Extensions
 
-* [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 generation or automatic validation (Future plan)
+#### Automatic validation
 
-+ [c2ffi](https://github.com/rpav/c2ffi) is a tool to create JSON format metadata from C header files. It is planned to use c2ffi to automatically generate bindings or tests.
+In the `script` directory, there are several tools to help implement ruby-htslib. Scripts using c2ffi can check the coverage of htslib functions in Ruby-htslib. They are useful when new versions of htslib are released.
 
-## Contributing
+- [c2ffi](https://github.com/rpav/c2ffi) is a tool to create JSON format metadata from C header files.
 
-Ruby-htslib is a library under development, so even small improvements like typofix are welcome! Please feel free to send us your pull requests.
+## Contributing
 
-* [Report bugs](https://github.com/kojix2/ruby-htslib/issues)
-* Fix bugs and [submit pull requests](https://github.com/kojix2/ruby-htslib/pulls)
-* Write, clarify, or fix documentation
-* Suggest or add new features
-* [financial contributions](https://github.com/sponsors/kojix2)
+Ruby-htslib is a library under development, so even minor improvements like typo fixes are welcome! Please feel free to send us your pull requests.
 
+- [Report bugs](https://github.com/kojix2/ruby-htslib/issues)
+- Fix bugs and [submit pull requests](https://github.com/kojix2/ruby-htslib/pulls)
+- Write, clarify, or fix documentation
+- Suggest or add new features
+- [financial contributions](https://github.com/sponsors/kojix2)
 
-```
+```markdown
 # Ownership and Commitment Rights
 
-Do you need commit rights to ruby-htslib repository?
+Do you need commit rights to the ruby-htslib repository?
 Do you want to get admin rights and take over the project?
 If so, please feel free to contact us @kojix2.
 ```
 
-#### Why do you implement htslib in a language like Ruby, which is not widely used in the bioinformatics?
+#### Why do you implement htslib in a language like Ruby, which is not widely used in bioinformatics?
 
-One of the greatest joys of using a minor language like Ruby in bioinformatics is that there is nothing stopping you from reinventing the wheel. Reinventing the wheel can be fun. But with languages like Python and R, where many bioinformatics masters work, there is no chance left for beginners to create htslib bindings. Bioinformatics file formats, libraries and tools are very complex and I don't know how to understand them. So I wanted to implement the HTSLib binding myself to better understand how the pioneers of bioinformatics felt when establishing the file format and how they created their tools. I hope one day we can work on bioinformatics using Ruby and Crystal languages, not to replace other languages such as Python and R, but to add new power and value to this advancing field.
+One of the greatest joys of using a minor language like Ruby in bioinformatics is that nothing stops you from reinventing the wheel. Reinventing the wheel can be fun. But with languages like Python and R, where many bioinformatics masters work, there is no chance for beginners to create htslib bindings. Bioinformatics file formats, libraries, and tools are very complex, and I need to learn how to understand them. So I started to implement the HTSLib binding myself to better understand how the pioneers of bioinformatics felt when establishing the file format and how they created their tools. I hope one day we can work on bioinformatics using Ruby and Crystal languages, not to replace other languages such as Python and R, but to add new power and value to this advancing field.
 
 ## Links
 
-* [samtools/hts-spec](https://github.com/samtools/hts-specs)
-* [bioruby](https://github.com/bioruby/bioruby)
+- [samtools/hts-spec](https://github.com/samtools/hts-specs)
+- [bioruby](https://github.com/bioruby/bioruby)
 
 ## Funding support
 
 This work was supported partially by [Ruby Association Grant 2020](https://www.ruby.or.jp/en/news/20201022).
+
 ## License
 
 [MIT License](https://opensource.org/licenses/MIT).

data/TUTORIAL.md

@@ -0,0 +1,270 @@
+# Tutorial
+
+```mermaid
+%%{init:{'theme':'base'}}%%
+classDiagram
+Bam~Hts~ o-- `Bam::Header`
+Bam o-- `Bam::Record`
+`Bam::Record` o-- `Bam::Header`
+Bcf~Hts~ o-- `Bcf::Header`
+Bcf o-- `Bcf::Record`
+`Bcf::Record` o--`Bcf::Header`
+`Bam::Header` o-- `Bam::HeaderRecord`
+`Bcf::Header` o-- `Bcf::HeaderRecord`
+`Bam::Record` o-- Flag
+`Bam::Record` o-- Cigar
+`Bam::Record` o-- Aux
+`Bcf::Record` o-- Info
+`Bcf::Record` o-- Format
+class Bam{
+  +@hts_file : FFI::Struct
+  +@header : Bam::Header
+  +@file_name
+  +@index_name
+  +@mode
+  +struct()
+  +build_index()
+  +each() Enumerable
+  +query()
+}
+class Bcf{
+  +@hts_file : FFI::Struct
+  +@header : Bcf::Header
+  +@file_name
+  +@index_name
+  +@mode
+  +struct()
+  +build_index()
+  +each() Enumerable
+  +query()
+}
+class Tbx~Hts~{
+  +@hts_file : FFI::Struct
+}
+class `Bam::Header`{
+  +@sam_hdr : FFI::Struct
+  +struct()
+  +target_count()
+  +target_names()
+  +to_s()
+}
+class `Bam::Record` {
+  +@bam1 : FFI::Struct
+  +@header : Bam::Header
+  +struct()
+  +tid()
+  +tid=()
+  +mtid()
+  +mtid=()
+  +pos()
+  +pos=()
+  +mpos()
+  +mpos=()
+  +bin()
+  +bin=()
+  +qname()
+  +flag()
+  +chorm()
+  +mapq()
+  +cigar()
+  +mate_chrom()
+  +isize()
+  +seq()
+  +qual()
+  +qual_string()
+  +aux()
+  +to_s()
+}
+class `Aux` {
+  -@record : Bam::Record
+  +[]()
+  +get_int()
+  +get_float()
+  +get_string()
+}
+class `Bcf::Header`{
+  +@bcf_hdr : FFI::Struct
+  +struct()
+  +to_s()
+}
+class `Bcf::Record`{
+  +@bcf1 : FFI::Struct
+  +@header : Bcf::Header
+  +struct()
+  +chrom()
+  +pos()
+  +id()
+  +qual()
+  +ref()
+  +alt()
+  +filter()
+  +info()
+  +format()
+  +to_s()
+}
+class Flag {
+  +@value : Integer
+  +paired?()
+  +proper_pair?()
+  +unmapped?()
+  +mate_unmapped?()
+  +reverse?()
+  +mate_reverse?()
+  +read1?()
+  +read2?()
+  +secondary?()
+  +qcfail?()
+  +duplicate?()
+  +supplementary?()
+  +&()
+  +|()
+  +^()
+  +~()
+  +<<()
+  +>>()
+  +to_i()
+  +to_s()
+}
+class Info {
+  -@record : Bcf::Record
+  +[]()
+  +get_int()
+  +get_float()
+  +get_string()
+  +get_flag()
+  +fields()
+  +length() +size()
+  +to_h()
+  -info_ptr()
+}
+class Format {
+  -@record : Bcf::Record
+  +[]()\
+  +get_int()
+  +get_float()
+  +get_string()
+  +get_flag()
+  +fields()
+  +length() +size()
+  +to_h()
+  -format_ptr()
+}
+class Cigar {
+  -@array : Array
+  +each() Enumerable
+  +qlen()
+  +rlen()
+  +to_s()
+  +==()
+  +eql?()
+}
+class Faidx{
+  +@fai
+}
+
+```
+
+## HTS::Bam - SAM / BAM / CRAM - Sequence Alignment Map file
+
+Reading fields
+
+```ruby
+require 'htslib'
+
+bam = HTS::Bam.open("test/fixtures/moo.bam")
+
+bam.each do |r|
+  pp name: r.qname,
+     flag: r.flag,
+     chrm: r.chrom,
+     strt: r.pos + 1,
+     mapq: r.mapq,
+     cigr: r.cigar.to_s,
+     mchr: r.mate_chrom,
+     mpos: r.mpos + 1,
+     isiz: r.isize,
+     seqs: r.seq,
+     qual: r.qual_string,
+     MC:   r.aux("MC")
+end
+
+bam.close
+```
+
+Open with block
+
+```ruby
+HTS::Bam.open("test/fixtures/moo.bam") do |b|
+  b.
+  do |r|
+    # ...
+  end
+end
+```
+
+Writing
+
+```ruby
+in = HTS::Bam.open("foo.bam")
+out = HTS::Bam.open("bar.bam", "wb")
+
+out.header = in.header
+# out.write_header(in.header)
+
+in.each do |r|
+  out << r
+  # out.write(r)
+end
+
+in.close
+out.close
+```
+
+## HTS::Bcf - VCF / BCF - Variant Call Format file
+
+Reading fields
+
+```ruby
+bcf = HTS::Bcf.open("b.bcf")
+
+bcf.each do |r|
+  p chrom:  r.chrom,
+    pos:    r.pos,
+    id:     r.id,
+    qual:   r.qual.round(2),
+    ref:    r.ref,
+    alt:    r.alt,
+    filter: r.filter,
+    info:   r.info.to_h,
+    format: r.format.to_h
+end
+
+bcf.close
+```
+
+Open with block
+
+```ruby
+HTS::Bcf.open("b.bcf") do |b|
+  b.each do |r|
+    # ...
+  end
+end
+```
+
+Writing
+
+```ruby
+in = HTS::Bcf.open("foo.bcf")
+out = HTS::Bcf.open("bar.bcf", "wb")
+
+out.header = in.header
+# out.write_header(in.header)
+in.each do |r|
+  out << r
+  # out.write(r)
+end
+
+in.close
+out.close
+```

data/lib/hts/bam/auxi.rb

@@ -4,21 +4,32 @@
 #
 # A. This is for compatibility with Windows.
 # In Windows, aux is a reserved word
-# You cannot create a file named aux.
+# You cannot create a file named aux. Eww!
 
 module HTS
   class Bam < Hts
     # Auxiliary record data
+    #
+    # @noge Aux is a View object.
+    # The result of the alignment is assigned to the bam1 structure.
+    # 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
+      attr_reader :record
+
       def initialize(record)
         @record = record
       end
 
+      # @note Why is this method named "get" instead of "fetch"?
+      # This is for compatibility with the Crystal language
+      # which provides methods like `get_int`, `get_float`, etc.
+      # I think they are better than `fetch_int`` and `fetch_float`.
       def get(key, type = nil)
         aux = LibHTS.bam_aux_get(@record.struct, key)
         return nil if aux.null?
 
-        type ||= aux.read_string(1)
+        type = type ? type.to_s : aux.read_string(1)
 
         # A (character), B (general array),
         # f (real number), H (hexadecimal array),
@@ -38,6 +49,21 @@ module HTS
         end
       end
 
+      # For compatibility with HTS.cr.
+      def get_int(key)
+        get(key, "i")
+      end
+
+      # For compatibility with HTS.cr.
+      def get_float(key)
+        get(key, "f")
+      end
+
+      # For compatibility with HTS.cr.
+      def get_string(key)
+        get(key, "Z")
+      end
+
       def [](key)
         get(key)
       end

data/lib/hts/bam/cigar.rb

@@ -6,11 +6,31 @@ module HTS
     class Cigar
       include Enumerable
 
-      def initialize(pointer, n_cigar)
-        @n_cigar = n_cigar
-        # Read the pointer before the memory is changed.
-        # Especially when called from a block of `each` iterator.
-        @c = pointer.read_array_of_uint32(n_cigar)
+      # a uint32_t array (with 32 bits for every CIGAR op: length<<4|operation)
+      attr_accessor :array
+
+      # Create a new Cigar object from a string.
+      # @param [String] cigar_str
+      # The CIGAR string is converted to a uint32_t array in htslib.
+      def self.parse(str)
+        c = FFI::MemoryPointer.new(:pointer)
+        m = FFI::MemoryPointer.new(:size_t)
+        LibHTS.sam_parse_cigar(str, FFI::Pointer::NULL, c, m)
+        cigar_array = c.read_pointer.read_array_of_uint32(m.read(:size_t))
+        obj = new
+        obj.array = cigar_array
+        obj
+      end
+
+      def initialize(record = nil)
+        if record
+          # The record is used at initialization and is not retained after that.
+          bam1 = record.struct
+          n_cigar = bam1[:core][:n_cigar]
+          @array = LibHTS.bam_get_cigar(bam1).read_array_of_uint32(n_cigar)
+        else
+          @array = []
+        end
       end
 
       def to_s
@@ -20,12 +40,32 @@ module HTS
       def each
         return to_enum(__method__) unless block_given?
 
-        @c.each do |c|
+        @array.each do |c|
           op =  LibHTS.bam_cigar_opchr(c)
           len = LibHTS.bam_cigar_oplen(c)
           yield [op, len]
         end
       end
+
+      def qlen
+        a = FFI::MemoryPointer.new(:uint32, @array.size)
+        a.write_array_of_uint32(@array)
+        LibHTS.bam_cigar2qlen(@array.size, a)
+      end
+
+      def rlen
+        a = FFI::MemoryPointer.new(:uint32, @array.size)
+        a.write_array_of_uint32(@array)
+        LibHTS.bam_cigar2rlen(@array.size, a)
+      end
+
+      def ==(other)
+        other.is_a?(Cigar) && (@array == other.array)
+      end
+
+      def eql?(other)
+        other.is_a?(Cigar) && @array.eql?(other.array)
+      end
     end
   end
 end

data/lib/hts/bam/flag.rb

@@ -28,8 +28,6 @@ module HTS
       # BAM_FDUP           = 1024
       # BAM_FSUPPLEMENTARY = 2048
 
-      # TODO: Enabling bitwise operations?
-
       TABLE = { paired?: LibHTS::BAM_FPAIRED,
                 proper_pair?: LibHTS::BAM_FPROPER_PAIR,
                 unmapped?: LibHTS::BAM_FUNMAP,
@@ -43,16 +41,57 @@ module HTS
                 duplicate?: LibHTS::BAM_FDUP,
                 supplementary?: LibHTS::BAM_FSUPPLEMENTARY }.freeze
 
-      TABLE.each do |name, v|
+      # @!macro [attach] generate_flag_methods
+      #   @!method $1
+      #   @return [Boolean]
+      def self.generate(name)
         define_method(name) do
-          has_flag?(v)
+          (@value & TABLE[name]) != 0
         end
       end
+      private_class_method :generate
+
+      generate :paired?
+      generate :proper_pair?
+      generate :unmapped?
+      generate :mate_unmapped?
+      generate :reverse?
+      generate :mate_reverse?
+      generate :read1?
+      generate :read2?
+      generate :secondary?
+      generate :qcfail?
+      generate :duplicate?
+      generate :supplementary?
 
       def has_flag?(f)
         (@value & f) != 0
       end
 
+      def &(other)
+        Flag.new(@value & other.to_i)
+      end
+
+      def |(other)
+        Flag.new(@value | other.to_i)
+      end
+
+      def ^(other)
+        Flag.new(@value ^ other.to_i)
+      end
+
+      def ~
+        Flag.new(~@value)
+      end
+
+      def <<(f)
+        Flag.new(@value << f.to_i)
+      end
+
+      def >>(other)
+        Flag.new(@value >> other.to_i)
+      end
+
       def to_i
         @value
       end