htslib 0.4.0 → 0.4.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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+  data.tar.gz: 060c7e5af8127c496af3b5d5bec5eca5e7476cb34ccc86a75546fd1a80d6dd8a
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+  data.tar.gz: 2a6bd47a73ff2695a515e934fa1919d8fcdf1108e10178404af31da769b4e7c40a8580f2382ab8f7e6ac8697261344fb32ecebc138807d5cd03724745457f4d4

data/lib/hts/bam/auxi.rb

@@ -248,10 +248,9 @@ module HTS
         end
       end
 
-      # Iterate auxiliary tags with their SAM/BAM type.
+      # Iterate auxiliary tags as key-value pairs.
       #
       # @yieldparam tag [String] 2-byte AUX tag name
-      # @yieldparam type [String] AUX type, e.g. "i", "Z", or "B:C"
       # @yieldparam value [Object] Ruby representation of the AUX value
       def each
         return enum_for(__method__) unless block_given?
@@ -261,7 +260,7 @@ module HTS
 
         loop do
           tag = FFI::Pointer.new(aux_ptr.address - 2).read_string(2)
-          yield tag, aux_type(aux_ptr), get_ruby_aux(aux_ptr)
+          yield tag, get_ruby_aux(aux_ptr)
           aux_ptr = LibHTS.bam_aux_next(@record.struct, aux_ptr)
           break if aux_ptr.null?
         end
@@ -269,6 +268,25 @@ module HTS
 
       alias each_pair each
 
+      # Iterate auxiliary tags with their SAM/BAM type.
+      #
+      # @yieldparam tag [String] 2-byte AUX tag name
+      # @yieldparam type [String] AUX type, e.g. "i", "Z", or "B:C"
+      # @yieldparam value [Object] Ruby representation of the AUX value
+      def each_with_type
+        return enum_for(__method__) unless block_given?
+
+        aux_ptr = first_pointer
+        return nil if aux_ptr.null?
+
+        loop do
+          tag = FFI::Pointer.new(aux_ptr.address - 2).read_string(2)
+          yield tag, aux_type(aux_ptr), get_ruby_aux(aux_ptr)
+          aux_ptr = LibHTS.bam_aux_next(@record.struct, aux_ptr)
+          break if aux_ptr.null?
+        end
+      end
+
       def to_h
         h = {}
         aux_ptr = first_pointer

data/lib/hts/bcf/header.rb

@@ -104,7 +104,6 @@ module HTS
         subset_samples = normalize_subset_samples(samples)
         validate_subset_samples!(subset_samples)
 
-        nil
         imap_pointer = nil
         if subset_samples.empty?
           subset_hdr = LibHTS.bcf_hdr_subset(@bcf_hdr, 0, ::FFI::Pointer::NULL, ::FFI::Pointer::NULL)

data/lib/hts/bcf.rb

@@ -322,7 +322,7 @@ module HTS
       record = Record.new(header, bcf1)
       begin
         loop do
-          slen = LibHTS.hts_itr_next(@hts_file[:fp][:bgzf], qiter, bcf1, ::FFI::Pointer::NULL)
+          slen = LibHTS.bcf_itr_next(@hts_file, qiter, bcf1)
           break if slen == -1
           raise if slen < -1
 
@@ -371,7 +371,7 @@ module HTS
       bcf1 = LibHTS.bcf_init
       record = Record.new(header, bcf1)
       loop do
-        slen = LibHTS.hts_itr_next(@hts_file[:fp][:bgzf], qiter, bcf1, ::FFI::Pointer::NULL)
+        slen = LibHTS.bcf_itr_next(@hts_file, qiter, bcf1)
         break if slen == -1
         raise if slen < -1
 

data/lib/hts/libhts/hfile.rb

@@ -64,6 +64,18 @@ module HTS
       [:string, :int, HFile],
       :string
 
+    # Read a line from a stream and append it to a kstring
+    attach_function \
+      :khgetline,
+      [KString, HFile],
+      :int
+
+    # Convenience function to call kgetline with a FILE *
+    attach_function \
+      :kfgetline,
+      [KString, :pointer],
+      :int
+
     # Peek at characters to be read without removing them from buffers
     attach_function \
       :hpeek,

data/lib/hts/libhts/tbx.rb

@@ -14,6 +14,21 @@ module HTS
       [Tbx, :string],
       :int
 
+    attach_function \
+      :tbx_itr_querys1,
+      [Tbx, :string],
+      HtsItr.by_ref
+
+    attach_function \
+      :tbx_itr_regarray,
+      [Tbx, :pointer, :uint],
+      HtsItr.by_ref
+
+    attach_function \
+      :tbx_itr_next1,
+      [HtsFile, Tbx, HtsItr, :pointer],
+      :int
+
     # Internal helper function used by tbx_itr_next()
     attach_function \
       :hts_get_bgzfp,

data/lib/hts/libhts/tbx_funcs.rb

@@ -16,11 +16,15 @@ module HTS
       end
 
       def tbx_itr_querys(tbx, s)
+        return tbx_itr_querys1(tbx, s) if respond_to?(:tbx_itr_querys1)
+
         hts_itr_querys(tbx[:idx], s, @@tbx_name2id, tbx, @ffi_functions[:hts_itr_query],
                        @ffi_functions[:tbx_readrec])
       end
 
       def tbx_itr_next(htsfp, tbx, itr, r)
+        return tbx_itr_next1(htsfp, tbx, itr, r) if respond_to?(:tbx_itr_next1)
+
         hts_itr_next(hts_get_bgzfp(htsfp), itr, r, tbx)
       end
 

data/lib/hts/libhts/vcf.rb

@@ -145,6 +145,16 @@ module HTS
       [BGZF, :pointer, :pointer, :pointer, :hts_pos_t, :hts_pos_t],
       :int
 
+    attach_function \
+      :bcf_itr_querys1,
+      [HtsIdx, BcfHdr, :string],
+      HtsItr.by_ref
+
+    attach_function \
+      :bcf_itr_regarray,
+      [HtsIdx, BcfHdr, :pointer, :uint],
+      HtsItr.by_ref
+
     # Write a line to a VCF file
     attach_function \
       :vcf_write_line,

data/lib/hts/libhts/vcf_funcs.rb

@@ -309,9 +309,22 @@ module HTS
       end
 
       def bcf_itr_querys(idx, hdr, s)
+        return bcf_itr_querys1(idx, hdr, s) if respond_to?(:bcf_itr_querys1)
+
         hts_itr_querys(idx, s, @@bcf_hdr_name2id, hdr, @ffi_functions[:hts_itr_query], @ffi_functions[:bcf_readrec])
       end
 
+      # Ruby implementation of htslib's static inline bcf_itr_next().
+      def bcf_itr_next(htsfp, itr, r)
+        return -2 unless htsfp[:is_bgzf] == 1
+
+        if itr[:multi] == 1
+          hts_itr_multi_next(htsfp, itr, r)
+        else
+          hts_itr_next(htsfp[:fp][:bgzf], itr, r, FFI::Pointer::NULL)
+        end
+      end
+
       # Load a BCF index
       def bcf_index_load(fn)
         hts_idx_load(fn, HTS_FMT_CSI)

data/lib/hts/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module HTS
-  VERSION = "0.4.0"
+  VERSION = "0.4.2"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: htslib
 version: !ruby/object:Gem::Version
-  version: 0.4.0
+  version: 0.4.2
 platform: ruby
 authors:
 - kojix2