htslib 0.0.5 → 0.0.6

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 3eb6fbb228a9fa0642c55cdfa39d5189b311df191725954ae46b8dda135dc8c7
-  data.tar.gz: c90ad39aa4919cefa56e534a706bf9659bba9c6ad69eb374491092ce16ae93f6
+  metadata.gz: f05bc93a621f3d5fb8d06e44c20ac4a3a95c5f6e243df2aebc97e10125fcb779
+  data.tar.gz: 73e747aa0999e54b3c8f01b981b91c4e293167265276a24eac85ea0fd6b85c13
 SHA512:
-  metadata.gz: 392ea7c6acb5b86e9e1c1a29f066049c54954edfd277be30541aee433a7349f9d74df09e663ec0269f30d6b87ff47d66a4a668470d3aa536e25a2058cf963546
-  data.tar.gz: 9cc235f8876b8fd4339593eb84a0f2cb8b605b9c82b624cd0f97691b4109a672f55ae90447bba17fb5efcb8257279ad8c2d87234bca390b1624c7aa8f9a7014e
+  metadata.gz: 8d0f3f8bb9f7a9c063222fd2dc6463f58bdfd784aff39757921dda1c8d417023b024ca9f6c92d7f0eecd30b8064adb1b94966cf962cf9e0e56d67303de0a903b
+  data.tar.gz: 8ef35b7aef04bf2f51ae0ba110d9ffc81c26d7a0c97a821aa1274c04b31ec29515b33c278391494f6a0d8efc5e2d965060ccd190ee0f92a2ec3562fb59c49169

data/README.md

@@ -9,11 +9,12 @@
 :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.
+It will provide APIs to read and write file formats such as [SAM, BAM, VCF, and BCF](http://samtools.github.io/hts-specs/).
 
 :apple: Feel free to fork it out if you can develop it! 
 
 :bowtie: alpha stage.
+
 ## Requirements
 
 * [Ruby](https://github.com/ruby/ruby) 2.7 or above.
@@ -92,8 +93,8 @@ bundle exec rake htslib:build
 bundle exec rake test
 ```
 
-We plan to actively use the new features of Ruby. Since the number of users is small, backward compatibility is not important.
-On the other hand, we will consider compatibility with [Crystal](https://github.com/bio-crystal/htslib.cr) to some extent.
+* Actively use the advanced features of Ruby.
+* Consider compatibility with [htslib.cr](https://github.com/bio-crystal/htslib.cr) to some extent.
 
 #### FFI Extensions
 

data/lib/hts/bam/cigar.rb

@@ -22,6 +22,8 @@ module HTS
       end
 
       def each
+        return to_enum(__method__) unless block_given?
+
         @n_cigar.times do |i|
           c = @pointer[i].read_uint32
           yield [LibHTS.bam_cigar_oplen(c),

data/lib/hts/bam/flag.rb

@@ -85,8 +85,12 @@ module HTS
         has_flag? LibHTS::BAM_FSUPPLEMENTARY
       end
 
-      def has_flag?(o)
-        @value[o] != 0
+      def has_flag?(m)
+        (@value & m) != 0
+      end
+
+      def to_s
+        "0x#{format('%x', @value)}\t#{@value}\t#{LibHTS.bam_flag2str(@value)}"
       end
     end
   end

data/lib/hts/bam/header.rb

@@ -18,6 +18,10 @@ module HTS
         @sam_hdr.to_ptr
       end
 
+      def target_count
+        @sam_hdr[:n_targets]
+      end
+
       # FIXME: better name?
       def seqs
         Array.new(@sam_hdr[:n_targets]) do |i|
@@ -25,7 +29,7 @@ module HTS
         end
       end
 
-      def text
+      def to_s
         LibHTS.sam_hdr_str(@sam_hdr)
       end
     end

data/lib/hts/bam/record.rb

@@ -69,7 +69,6 @@ module HTS
 
       # returns the chromosome or '' if not mapped.
       def chrom
-        tid = @bam1[:core][:tid]
         return "" if tid == -1
 
         LibHTS.sam_hdr_tid2name(@header, tid)
@@ -77,10 +76,10 @@ module HTS
 
       # returns the chromosome of the mate or '' if not mapped.
       def mate_chrom
-        tid = @bam1[:core][:mtid]
-        return "" if tid == -1
+        mtid = mate_tid
+        return "" if mtid == -1
 
-        LibHTS.sam_hdr_tid2name(@header, tid)
+        LibHTS.sam_hdr_tid2name(@header, mtid)
       end
 
       def strand
@@ -168,6 +167,11 @@ module HTS
         return nil if aux.null?
 
         t = aux.read_string(1)
+
+        # A (character), B (general array),
+        # f (real number), H (hexadecimal array),
+        # i (integer), or Z (string).
+
         case t
         when "i", "I", "c", "C", "s", "S"
           LibHTS.bam_aux2i(aux)
@@ -175,8 +179,8 @@ module HTS
           LibHTS.bam_aux2f(aux)
         when "Z", "H"
           LibHTS.bam_aux2Z(aux)
-        when "A"
-          LibHTS.bam_aux2A(aux)
+        when "A" # char
+          LibHTS.bam_aux2A(aux).chr
         end
       end
 

data/lib/hts/bcf/format.rb

@@ -36,8 +36,9 @@ module HTS
           format_values.call(LibHTS::BCF_HT_FLAG)
                        .read_int == 1
         when :string, :str
+          raise NotImplementedError, "String type not implemented yet."
           format_values.call(LibHTS::BCF_HT_STR)
-                       .read_pointer.read_string
+                       .read_string
         end
       end
 

data/lib/hts/bcf/header.rb

@@ -3,16 +3,23 @@
 module HTS
   class Bcf
     class Header
-      def initialize(h)
-        @h = h
+      def initialize(bcf_hdr)
+        @bcf_hdr = bcf_hdr
       end
 
       def struct
-        @h
+        @bcf_hdr
       end
 
       def to_ptr
-        @h.to_ptr
+        @bcf_hdr.to_ptr
+      end
+
+      def to_s
+        kstr = LibHTS::KString.new
+        raise "Failed to get header string" unless LibHTS.bcf_hdr_format(@bcf_hdr, 0, kstr)
+
+        kstr[:s]
       end
     end
   end

data/lib/hts/bcf/info.rb

@@ -44,6 +44,7 @@ module HTS
         end
       end
 
+      # FIXME: naming? room for improvement.
       def fields
         n_info = @record.struct[:n_info]
         Array.new(n_info) do |i|

data/lib/hts/bcf/record.rb

@@ -16,7 +16,7 @@ module HTS
       end
 
       def to_ptr
-        @bcf.to_ptr
+        @bcf1.to_ptr
       end
 
       # def inspect; end
@@ -64,6 +64,8 @@ module HTS
           d[:flt].get_array_of_int(0, n_flt).map do |i|
             LibHTS.bcf_hdr_int2id(@bcf.header.struct, LibHTS::BCF_DT_ID, i)
           end
+        else
+          raise "Unexpected number of filters. n_flt: #{n_flt}"
         end
       end
 
@@ -80,13 +82,14 @@ module HTS
         LibHTS.bcf_unpack(@bcf1, LibHTS::BCF_UN_STR)
         @bcf1[:d][:allele].get_array_of_pointer(
           FFI::TYPE_POINTER.size, @bcf1[:n_allele] - 1
-        ).map { |c| c.read_string }
+        ).map(&:read_string)
       end
 
       def alleles
+        LibHTS.bcf_unpack(@bcf1, LibHTS::BCF_UN_STR)
         @bcf1[:d][:allele].get_array_of_pointer(
           0, @bcf1[:n_allele]
-        ).map { |c| c.read_string }
+        ).map(&:read_string)
       end
 
       def info

data/lib/hts/bcf.rb

@@ -66,7 +66,7 @@ module HTS
       self
     end
 
-    def n_samples
+    def sample_count
       LibHTS.bcf_hdr_nsamples(header.struct)
     end
   end

data/lib/hts/ffi_ext/struct.rb

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

data/lib/hts/libhts/hts.rb

@@ -89,6 +89,12 @@ module HTS
       %i[HFILE string string],
       HtsFile.by_ref
 
+    # For output streams, flush any buffered data
+    attach_function \
+      :hts_flush,
+      [HtsFile],
+      :int
+
     # Close a file handle, flushing buffered data for output streams
     attach_function \
       :hts_close,