htslib 0.2.9 → 0.3.1

data/lib/hts/libhts/sam.rb

@@ -2,6 +2,11 @@
 
 module HTS
   module LibHTS
+    # Callback type for bam_plp_auto_f: int (*)(void *data, bam1_t *b)
+    # Use raw pointer for bam1_t to avoid creating ManagedStruct wrappers (which would double-free)
+    callback :bam_plp_auto_f, %i[pointer pointer], :int
+    # callback :bam_plp_auto_f, [:pointer, Bam1.by_ref], :int
+
     # Generates a new unpopulated header structure.
     attach_function \
       :sam_hdr_init,
@@ -414,24 +419,24 @@ module HTS
 
     attach_function \
       :sam_parse1,
-      [KString, SamHdr, Bam1],
+      [KString, SamHdr, :pointer], # [KString, SamHdr, (Bam1 | Bam1View)]
       :int
 
     attach_function \
       :sam_format1,
-      [SamHdr, Bam1, KString],
+      [SamHdr, :pointer, KString], # [SamHdr, (Bam1 | Bam1View), KString]
       :int
 
     # Read a record from a file
     attach_function \
       :sam_read1,
-      [HtsFile, SamHdr, Bam1],
+      [HtsFile, SamHdr, :pointer], # [HtsFile, SamHdr, (Bam1 | Bam1View)]
       :int
 
     # Write a record to a file
     attach_function \
       :sam_write1,
-      [HtsFile, SamHdr, Bam1],
+      [HtsFile, SamHdr, :pointer], # [HtsFile, SamHdr, (Bam1 | Bam1View)]
       :int
 
     # Checks whether a record passes an hts_filter.
@@ -555,28 +560,28 @@ module HTS
 
     attach_function \
       :bam_plp_push,
-      [:bam_plp, Bam1],
+      [:bam_plp, Bam1.by_ref],
       :int
 
     attach_function \
       :bam_plp_next,
       %i[bam_plp pointer pointer pointer],
-      BamPileup1.by_ref
+      :pointer # BamPileup1.by_ref
 
     attach_function \
       :bam_plp_auto,
       %i[bam_plp pointer pointer pointer],
-      BamPileup1.by_ref
+      :pointer # BamPileup1.by_ref
 
     attach_function \
       :bam_plp64_next,
       %i[bam_plp pointer pointer pointer],
-      BamPileup1.by_ref
+      :pointer # BamPileup1.by_ref
 
     attach_function \
       :bam_plp64_auto,
       %i[bam_plp pointer pointer pointer],
-      BamPileup1.by_ref
+      :pointer # BamPileup1.by_ref
 
     attach_function \
       :bam_plp_set_maxcnt,
@@ -588,7 +593,9 @@ module HTS
       [:bam_plp],
       :void
 
-    callback :bam_plp_callback_function, [:pointer, Bam1, BamPileupCd], :int
+    # Callback type for constructor/destructor: int (*)(void *data, const bam1_t *b, bam_pileup_cd *cd)
+    callback :bam_plp_callback_function, [:pointer, :pointer, BamPileupCd.by_ref], :int
+    # callback :bam_plp_callback_function, [:pointer, Bam1.by_ref, BamPileupCd.by_ref], :int
 
     # sets a callback to initialise any per-pileup1_t fields.
     attach_function \
@@ -602,17 +609,21 @@ module HTS
       :void
 
     # Get pileup padded insertion sequence
+    # Make pointer passing explicit by using by_ref for structs
     attach_function \
       :bam_plp_insertion,
-      [BamPileup1, KString, :pointer],
+      [BamPileup1.by_ref, KString.by_ref, :pointer],
       :int
 
     # Get pileup padded insertion sequence, including base modifications
     attach_function \
       :bam_plp_insertion_mod,
-      [BamPileup1, :pointer, KString, :pointer],
+      [BamPileup1.by_ref, HtsBaseModState, KString.by_ref, :pointer],
       :int
 
+    # NOTE: There is no bam_plp_init_overlaps in HTSlib (only bam_mplp_init_overlaps exists).
+    # The incorrect binding is removed to avoid undefined symbol errors.
+
     attach_function \
       :bam_mplp_init,
       %i[int bam_plp_auto_f pointer],
@@ -672,61 +683,61 @@ module HTS
     attach_function \
       :hts_base_mod_state_alloc,
       [],
-      :pointer # hts_base_mod_state
+      HtsBaseModState
 
     # Destroys an  hts_base_mode_state.
     attach_function \
       :hts_base_mod_state_free,
-      [:pointer], # hts_base_mod_state
+      [HtsBaseModState],
       :void
 
     # Parses the MM and ML tags out of a bam record.
     attach_function \
       :bam_parse_basemod,
-      [Bam1, :pointer],
+      [Bam1, HtsBaseModState],
       :int
 
     # Parses the MM and ML tags out of a bam record.
     attach_function \
       :bam_parse_basemod2,
-      [Bam1, :pointer, :uint32],
+      [Bam1, HtsBaseModState, :uint32],
       :int
 
     # Returns modification status for the next base position in the query seq.
     attach_function \
       :bam_mods_at_next_pos,
-      [Bam1, :pointer, :pointer, :int],
+      [Bam1, HtsBaseModState, :pointer, :int],
       :int
 
     # Finds the next location containing base modifications and returns them
     attach_function \
       :bam_next_basemod,
-      [Bam1, :pointer, :pointer, :int, :pointer],
+      [Bam1, HtsBaseModState, :pointer, :int, :pointer],
       :int
 
     # Returns modification status for a specific query position.
     attach_function \
       :bam_mods_at_qpos,
-      [Bam1, :int, :pointer, :pointer, :int],
+      [Bam1, :int, HtsBaseModState, :pointer, :int],
       :int
 
     # Returns data about a specific modification type for the alignment record.
     attach_function \
       :bam_mods_query_type,
-      %i[pointer int pointer pointer string],
+      [HtsBaseModState, :int, :pointer, :pointer, :pointer],
       :int
 
     # Returns data about the i^th modification type for the alignment record.
     attach_function \
       :bam_mods_queryi,
-      %i[pointer int pointer pointer string],
+      [HtsBaseModState, :int, :pointer, :pointer, :pointer],
       :int
 
     # Returns the list of base modification codes provided for this
     attach_function \
       :bam_mods_recorded,
-      %i[pointer pointer],
-      :int
+      [HtsBaseModState, :pointer],
+      :pointer
   end
 end
 

data/lib/hts/libhts/sam_funcs.rb

@@ -105,7 +105,7 @@ module HTS
 
       # Modifies a single base in the bam structure.
       def bam_set_seqi(s, i, b)
-        s[i >> 1] = (s[i >> 1] & (0xf0 >> ((~i & 1) << 2))) | ((b) << ((~i & 1) << 2))
+        s[i >> 1] = (s[i >> 1] & (0xf0 >> ((~i & 1) << 2))) | (b << ((~i & 1) << 2))
       end
 
       # Returns the SAM formatted text of the \@HD header line

data/lib/hts/libhts/vcf_funcs.rb

@@ -167,7 +167,7 @@ module HTS
 
       # Conversion between alleles indexes to Number=G genotype index (assuming diploid, all 0-based)
       def bcf_alleles2gt(a, b)
-        ((a) > (b) ? (a * (a + 1) / 2 + b) : (b * (b + 1) / 2 + a))
+        (a > b ? (a * (a + 1) / 2 + b) : (b * (b + 1) / 2 + a))
       end
 
       # Get INFO values

data/lib/hts/libhts.rb

@@ -23,6 +23,12 @@ module HTS
     rescue FFI::NotFoundError => e
       warn e.message if $VERBOSE
     end
+
+    def self.attach_variable(*)
+      super
+    rescue FFI::NotFoundError => e
+      warn e.message if $VERBOSE
+    end
   end
 end
 

data/lib/hts/tabix.rb

@@ -24,7 +24,7 @@ module HTS
 
     def initialize(file_name, index: nil, threads: nil, build_index: false)
       if block_given?
-        message = "HTS::Tabix.new() dose not take block; Please use HTS::Tabix.open() instead"
+        message = "HTS::Tabix.new() does not take block; Please use HTS::Tabix.open() instead"
         raise message
       end
 
@@ -44,8 +44,27 @@ module HTS
       @idx = load_index(index)
     end
 
-    def build_index
-      raise "Not implemented yet"
+    def build_index(index_name = nil, min_shift: 0)
+      check_closed
+
+      if index_name
+        warn "Create index for #{@file_name} to #{index_name}"
+        case LibHTS.tbx_index_build2(@file_name, index_name, min_shift, LibHTS.tbx_conf_vcf)
+        when 0 # successful
+        when -1 then raise "general failure"
+        when -2 then raise "compression not BGZF"
+        else raise "unknown error"
+        end
+      else
+        warn "Create index for #{@file_name}"
+        case LibHTS.tbx_index_build(@file_name, min_shift, LibHTS.tbx_conf_vcf)
+        when 0 # successful
+        when -1 then raise "general failure"
+        when -2 then raise "compression not BGZF"
+        else raise "unknown error"
+        end
+      end
+      self # for method chaining
     end
 
     def load_index(index_name = nil)

data/lib/hts/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module HTS
-  VERSION = "0.2.9"
+  VERSION = "0.3.1"
 end

metadata

@@ -1,14 +1,13 @@
 --- !ruby/object:Gem::Specification
 name: htslib
 version: !ruby/object:Gem::Version
-  version: 0.2.9
+  version: 0.3.1
 platform: ruby
 authors:
 - kojix2
-autorequire:
 bindir: bin
 cert_chain: []
-date: 2024-09-13 00:00:00.000000000 Z
+date: 1980-01-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -52,7 +51,6 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
-description:
 email:
 - 2xijok@gmail.com
 executables: []
@@ -64,10 +62,13 @@ files:
 - TUTORIAL.md
 - lib/hts/bam.rb
 - lib/hts/bam/auxi.rb
+- lib/hts/bam/base_mod.rb
 - lib/hts/bam/cigar.rb
 - lib/hts/bam/flag.rb
 - lib/hts/bam/header.rb
 - lib/hts/bam/header_record.rb
+- lib/hts/bam/mpileup.rb
+- lib/hts/bam/pileup.rb
 - lib/hts/bam/record.rb
 - lib/hts/bcf.rb
 - lib/hts/bcf/format.rb
@@ -104,7 +105,6 @@ licenses:
 - MIT
 metadata:
   msys2_mingw_dependencies: htslib
-post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -119,8 +119,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.5.11
-signing_key:
+rubygems_version: 3.6.9
 specification_version: 4
 summary: HTSlib bindings for Ruby
 test_files: []