htslib 0.0.6 → 0.1.0

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data/README.md

@@ -6,10 +6,7 @@
 [![DOI](https://zenodo.org/badge/247078205.svg)](https://zenodo.org/badge/latestdoi/247078205)
 [![Docs Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://rubydoc.info/gems/htslib)
 
-:dna: [HTSlib](https://github.com/samtools/htslib) - for Ruby
-
-Ruby-htslib is the Ruby bindings to HTSlib, a C library for processing high throughput sequencing (HTS) data. 
-It will provide APIs to read and write file formats such as [SAM, BAM, VCF, and BCF](http://samtools.github.io/hts-specs/).
+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! 
 
@@ -39,51 +36,80 @@ export HTSLIBDIR="/your/path/to/htslib" # libhts.so
 
 ## Overview
 
-### Low level API
+### High level API
 
-`HTS::LibHTS` provides native functions. 
+Read SAM / BAM / CRAM - Sequence Alignment Map file
 
 ```ruby
 require 'htslib'
 
-a = HTS::LibHTS.hts_open("a.bam", "r")
-b = HTS::LibHTS.hts_get_format(a)
-p b[:category]
-p b[:format]
+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.map { |i| (i + 33).chr }.join,
+     MC:   r.aux("MC")
+end
+
+bam.close
 ```
 
-Note: Managed struct is not used in ruby-htslib. You may need to free the memory by yourself.
+Read VCF / BCF - Variant Call Format file
+
+```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
 
-### High level API (Plan)
+bcf.close
+```
 
-`Cram` `Bam` `Bcf` `Faidx` `Tabix`
+### Low level API
 
-A high-level API is under development. We will change and improve the API to make it better.
+`HTS::LibHTS` provides native　C functions. 
 
 ```ruby
 require 'htslib'
 
-bam = HTS::Bam.new("a.bam")
-
-bam.each do |r|
-  p name:  r.qname,
-    flag:  r.flag,
-    start: r.start + 1,
-    mpos:  r.mate_pos + 1,
-    mqual: r.mapping_quality,
-    seq:   r.sequence,
-    cigar: r.cigar.to_s,
-    qual:  r.base_qualities.map { |i| (i + 33).chr }.join
-end
+a = HTS::LibHTS.hts_open("a.bam", "r")
+b = HTS::LibHTS.hts_get_format(a)
+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. 
+
+### 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. Crsytal language is not as flexible as Ruby language. You can not use eval methods, and you must always be aware of the types. It is not very suitable for writing one-time scripts or experimenting with different code. However, If you have already written code in ruby-htslib, have a clear idea of the manipulations you want to do, and need to execute them many times, then by all means try to implement the command line tool using htslib.cr. The Crystal language is very fast and can perform almost as well as the Rust and C languages.
+
 ## Documentation
 
+* [API Documentation (develop branch)](https://kojix2.github.io/ruby-htslib/)
 * [RubyDoc.info - HTSlib](https://rdoc.info/gems/htslib)
 
 ## Development
 
-To get started with development
+To get started with development:
 
 ```sh
 git clone --recursive https://github.com/kojix2/ruby-htslib
@@ -93,8 +119,13 @@ bundle exec rake htslib:build
 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.
+
 * Actively use the advanced features of Ruby.
-* Consider compatibility with [htslib.cr](https://github.com/bio-crystal/htslib.cr) to some extent.
+* Remain compatibile with [htslib.cr](https://github.com/bio-crystal/htslib.cr).
+  * The most difficult part is the return value. In the Crystal language, it is convenient for a method to return only one type. In the Ruby language, on the other hand, it is more convenient to return multiple classes. For example, in the Crystal language, it is confusing that a return value can take four types: Int32, Float32, Nil, and String. In Ruby, on the other hand, it is very common and does not cause any problems.
 
 #### FFI Extensions
 
@@ -114,6 +145,16 @@ Ruby-htslib is a library under development, so even small improvements like typo
 * Suggest or add new features
 * [financial contributions](https://github.com/sponsors/kojix2)
 
+```
+Do you need commit rights to 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?
+
+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. And that effort is still going on today...
+
 ## Links
 
 * [samtools/hts-spec](https://github.com/samtools/hts-specs)

data/lib/hts/bam/aux.rb

@@ -0,0 +1,39 @@
+# frozen_string_literal: true
+
+module HTS
+  class Bam < Hts
+    class Aux
+      def initialize(record)
+        @record = record
+      end
+
+      def get(key, type = nil)
+        aux = LibHTS.bam_aux_get(@record.struct, key)
+        return nil if aux.null?
+
+        type ||= 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
+      end
+
+      def [](key)
+        get(key)
+      end
+    end
+  end
+end

data/lib/hts/bam/cigar.rb

@@ -1,10 +1,7 @@
 # frozen_string_literal: true
 
-# Based on hts-python
-# https://github.com/quinlan-lab/hts-python
-
 module HTS
-  class Bam
+  class Bam < Hts
     class Cigar
       include Enumerable
 
@@ -18,7 +15,7 @@ module HTS
       end
 
       def to_s
-        to_a.flatten.join
+        map { |op, len| "#{len}#{op}" }.join
       end
 
       def each
@@ -26,8 +23,9 @@ module HTS
 
         @n_cigar.times do |i|
           c = @pointer[i].read_uint32
-          yield [LibHTS.bam_cigar_oplen(c),
-                 LibHTS.bam_cigar_opchr(c)]
+          op =  LibHTS.bam_cigar_opchr(c)
+          len = LibHTS.bam_cigar_oplen(c)
+          yield [op, len]
         end
       end
     end

data/lib/hts/bam/flag.rb

@@ -4,7 +4,7 @@
 # https://github.com/brentp/hts-nim/blob/master/src/hts/bam/flag.nim
 
 module HTS
-  class Bam
+  class Bam < Hts
     class Flag
       def initialize(flag_value)
         raise TypeError unless flag_value.is_a? Integer
@@ -27,70 +27,34 @@ module HTS
       # BAM_FDUP           = 1024
       # BAM_FSUPPLEMENTARY = 2048
 
-      # TODO: Enabling bitwise operations
-      # hts-nim
-      # proc `and`*(f: Flag, o: uint16): uint16 {. borrow, inline .}
-      # proc `and`*(f: Flag, o: Flag): uint16 {. borrow, inline .}
-      # proc `or`*(f: Flag, o: uint16): uint16 {. borrow .}
-      # proc `or`*(o: uint16, f: Flag): uint16 {. borrow .}
-      # proc `==`*(f: Flag, o: Flag): bool {. borrow, inline .}
-      # proc `==`*(f: Flag, o: uint16): bool {. borrow, inline .}
-      # proc `==`*(o: uint16, f: Flag): bool {. borrow, inline .}
+      # TODO: Enabling bitwise operations?
 
-      def paired?
-        has_flag? LibHTS::BAM_FPAIRED
-      end
-
-      def proper_pair?
-        has_flag? LibHTS::BAM_FPROPER_PAIR
-      end
-
-      def unmapped?
-        has_flag? LibHTS::BAM_FUNMAP
-      end
-
-      def mate_unmapped?
-        has_flag? LibHTS::BAM_FMUNMAP
-      end
-
-      def reverse?
-        has_flag? LibHTS::BAM_FREVERSE
-      end
-
-      def mate_reverse?
-        has_flag? LibHTS::BAM_FMREVERSE
-      end
-
-      def read1?
-        has_flag? LibHTS::BAM_FREAD1
-      end
-
-      def read2?
-        has_flag? LibHTS::BAM_FREAD2
-      end
-
-      def secondary?
-        has_flag? LibHTS::BAM_FSECONDARY
-      end
-
-      def qcfail?
-        has_flag? LibHTS::BAM_FQCFAIL
-      end
-
-      def dup?
-        has_flag? LibHTS::BAM_FDUP
-      end
+      TABLE = { paired?: LibHTS::BAM_FPAIRED,
+                proper_pair?: LibHTS::BAM_FPROPER_PAIR,
+                unmapped?: LibHTS::BAM_FUNMAP,
+                mate_unmapped?: LibHTS::BAM_FMUNMAP,
+                reverse?: LibHTS::BAM_FREVERSE,
+                mate_reverse?: LibHTS::BAM_FMREVERSE,
+                read1?: LibHTS::BAM_FREAD1,
+                read2?: LibHTS::BAM_FREAD2,
+                secondary?: LibHTS::BAM_FSECONDARY,
+                qcfail?: LibHTS::BAM_FQCFAIL,
+                duplicate?: LibHTS::BAM_FDUP,
+                supplementary?: LibHTS::BAM_FSUPPLEMENTARY }.freeze
 
-      def supplementary?
-        has_flag? LibHTS::BAM_FSUPPLEMENTARY
+      TABLE.each do |name, v|
+        define_method(name) do
+          has_flag?(v)
+        end
       end
 
-      def has_flag?(m)
-        (@value & m) != 0
+      def has_flag?(f)
+        (@value & f) != 0
       end
 
       def to_s
-        "0x#{format('%x', @value)}\t#{@value}\t#{LibHTS.bam_flag2str(@value)}"
+        LibHTS.bam_flag2str(@value)
+        # "0x#{format('%x', @value)}\t#{@value}\t#{LibHTS.bam_flag2str(@value)}"
       end
     end
   end

data/lib/hts/bam/header.rb

@@ -1,13 +1,10 @@
 # frozen_string_literal: true
 
-# Based on hts-python
-# https://github.com/quinlan-lab/hts-python
-
 module HTS
-  class Bam
+  class Bam < Hts
     class Header
-      def initialize(pointer)
-        @sam_hdr = pointer
+      def initialize(hts_file)
+        @sam_hdr = LibHTS.sam_hdr_read(hts_file)
       end
 
       def struct
@@ -22,16 +19,27 @@ module HTS
         @sam_hdr[:n_targets]
       end
 
-      # FIXME: better name?
-      def seqs
-        Array.new(@sam_hdr[:n_targets]) do |i|
+      def target_names
+        Array.new(target_count) do |i|
           LibHTS.sam_hdr_tid2name(@sam_hdr, i)
         end
       end
 
+      def target_len
+        Array.new(target_count) do |i|
+          LibHTS.sam_hdr_tid2len(@sam_hdr, i)
+        end
+      end
+
       def to_s
         LibHTS.sam_hdr_str(@sam_hdr)
       end
+
+      private
+
+      def initialize_copy(orig)
+        @sam_hdr = LibHTS.sam_hdr_dup(orig.struct)
+      end
     end
   end
 end

data/lib/hts/bam/record.rb

@@ -1,13 +1,16 @@
 # frozen_string_literal: true
 
-# Based on hts-python
-# https://github.com/quinlan-lab/hts-python
+require_relative "flag"
+require_relative "cigar"
+require_relative "aux"
 
 module HTS
-  class Bam
+  class Bam < Hts
     class Record
       SEQ_NT16_STR = "=ACMGRSVTWYHKDBN"
 
+      attr_reader :header
+
       def initialize(bam1_t, header)
         @bam1 = bam1_t
         @header = header
@@ -21,16 +24,6 @@ module HTS
         @bam1.to_ptr
       end
 
-      attr_reader :header
-
-      # def initialize_copy
-      #   super
-      # end
-
-      def self.rom_sam_str; end
-
-      def tags; end
-
       # returns the query name.
       def qname
         LibHTS.bam_get_qname(@bam1).read_string
@@ -46,26 +39,49 @@ module HTS
         @bam1[:core][:tid]
       end
 
+      def tid=(tid)
+        @bam1[:core][:tid] = tid
+      end
+
       # returns the tid of the mate or -1 if not mapped.
-      def mate_tid
+      def mtid
         @bam1[:core][:mtid]
       end
 
+      def mtid=(mtid)
+        @bam1[:core][:mtid] = mtid
+      end
+
       # returns 0-based start position.
-      def start
+      def pos
         @bam1[:core][:pos]
       end
 
-      # returns end position of the read.
-      def stop
-        LibHTS.bam_endpos @bam1
+      def pos=(pos)
+        @bam1[:core][:pos] = pos
       end
 
       # returns 0-based mate position
-      def mate_start
+      def mpos
         @bam1[:core][:mpos]
       end
-      alias mate_pos mate_start
+
+      def mpos=(mpos)
+        @bam1[:core][:mpos] = mpos
+      end
+
+      def bin
+        @bam1[:core][:bin]
+      end
+
+      def bin=(bin)
+        @bam1[:core][:bin] = bin
+      end
+
+      # returns end position of the read.
+      def endpos
+        LibHTS.bam_endpos @bam1
+      end
 
       # returns the chromosome or '' if not mapped.
       def chrom
@@ -74,32 +90,44 @@ module HTS
         LibHTS.sam_hdr_tid2name(@header, tid)
       end
 
+      alias contig chrom
+
       # returns the chromosome of the mate or '' if not mapped.
       def mate_chrom
-        mtid = mate_tid
         return "" if mtid == -1
 
         LibHTS.sam_hdr_tid2name(@header, mtid)
       end
 
+      alias mate_contig mate_chrom
+
+      # Get strand information.
       def strand
         LibHTS.bam_is_rev(@bam1) ? "-" : "+"
       end
 
-      # def start=(v)
-      #   raise 'Not Implemented'
-      # end
-
       # insert size
-      def isize
+      def insert_size
         @bam1[:core][:isize]
       end
 
+      alias isize insert_size
+
+      def insert_size=(isize)
+        @bam1[:core][:isize] = isize
+      end
+
+      alias isize= insert_size=
+
       # mapping quality
-      def mapping_quality
+      def mapq
         @bam1[:core][:qual]
       end
 
+      def mapq=(mapq)
+        @bam1[:core][:qual] = mapq
+      end
+
       # returns a `Cigar` object.
       def cigar
         Cigar.new(LibHTS.bam_get_cigar(@bam1), @bam1[:core][:n_cigar])
@@ -120,7 +148,7 @@ module HTS
       end
 
       # return the read sequence
-      def sequence
+      def seq
         r = LibHTS.bam_get_seq(@bam1)
         seq = String.new
         (@bam1[:core][:l_qseq]).times do |i|
@@ -128,59 +156,74 @@ module HTS
         end
         seq
       end
+      alias sequence seq
+
+      def len
+        @bam1[:core][:l_qseq]
+      end
 
       # return only the base of the requested index "i" of the query sequence.
-      def base_at(n)
+      def base(n)
         n += @bam1[:core][:l_qseq] if n < 0
-        return "." if (n >= @bam1[:core][:l_qseq]) || (n < 0) # eg. base_at(-1000)
+        return "." if (n >= @bam1[:core][:l_qseq]) || (n < 0) # eg. base(-1000)
 
         r = LibHTS.bam_get_seq(@bam1)
         SEQ_NT16_STR[LibHTS.bam_seqi(r, n)]
       end
 
       # return the base qualities
-      def base_qualities
+      def qual
         q_ptr = LibHTS.bam_get_qual(@bam1)
         q_ptr.read_array_of_uint8(@bam1[:core][:l_qseq])
       end
 
       # return only the base quality of the requested index "i" of the query sequence.
-      def base_quality_at(n)
+      def base_qual(n)
         n += @bam1[:core][:l_qseq] if n < 0
-        return 0 if (n >= @bam1[:core][:l_qseq]) || (n < 0) # eg. base_quality_at(-1000)
+        return 0 if (n >= @bam1[:core][:l_qseq]) || (n < 0) # eg. base_qual(-1000)
 
         q_ptr = LibHTS.bam_get_qual(@bam1)
         q_ptr.get_uint8(n)
       end
 
-      def flag_str
-        LibHTS.bam_flag2str(@bam1[:core][:flag])
-      end
-
       # returns a `Flag` object.
       def flag
         Flag.new(@bam1[:core][:flag])
       end
 
-      def tag(str)
-        aux = LibHTS.bam_aux_get(@bam1, str)
-        return nil if aux.null?
+      def flag=(flag)
+        case flag
+        when Integer
+          @bam1[:core][:flag] = flag
+        when Flag
+          @bam1[:core][:flag] = flag.value
+        else
+          raise "Invalid flag type: #{flag.class}"
+        end
+      end
+
+      # retruns the auxillary fields.
+      def aux(key = nil)
+        aux = Aux.new(self)
+        if key
+          aux.get(key)
+        else
+          aux
+        end
+      end
+
+      # TODO: add a method to get the auxillary fields as a hash.
 
-        t = aux.read_string(1)
+      # TODO: add a method to set the auxillary fields.
 
-        # A (character), B (general array),
-        # f (real number), H (hexadecimal array),
-        # i (integer), or Z (string).
+      # TODO: add a method to remove the auxillary fields.
 
-        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" # char
-          LibHTS.bam_aux2A(aux).chr
+      # TODO: add a method to set variable length data (qname, cigar, seq, qual).
+
+      # Calling flag is delegated to the Flag object.
+      Flag::TABLE.each_key do |m|
+        define_method(m) do
+          flag.send(m)
         end
       end
 
@@ -191,9 +234,12 @@ module HTS
         kstr[:s]
       end
 
-      # TODO:
-      # def eql?
-      # def hash
+      private
+
+      def initialize_copy(orig)
+        @header = orig.header
+        @bam = LibHTS.bam_dup1(orig.struct)
+      end
     end
   end
 end