htslib 0.0.5 → 0.0.6

data/lib/hts/libhts/vcf_funcs.rb

@@ -0,0 +1,430 @@
+# frozen_string_literal: true
+
+module HTS
+  module LibHTS
+    attach_function \
+      :bcf_hdr_init,
+      [:string],
+      BcfHdr.by_ref
+
+    attach_function \
+      :bcf_hdr_destroy,
+      [BcfHdr],
+      :void
+
+    attach_function \
+      :bcf_init,
+      [],
+      Bcf1.by_ref
+
+    attach_function \
+      :bcf_destroy,
+      [Bcf1],
+      :void
+
+    attach_function \
+      :bcf_empty,
+      [Bcf1],
+      :void
+
+    attach_function \
+      :bcf_clear,
+      [Bcf1],
+      :void
+
+    attach_function \
+      :bcf_hdr_read,
+      [HtsFile],
+      BcfHdr.by_ref
+
+    attach_function \
+      :bcf_hdr_set_samples,
+      [BcfHdr, :string, :int],
+      :int
+
+    attach_function \
+      :bcf_subset_format,
+      [BcfHdr, Bcf1],
+      :int
+
+    attach_function \
+      :bcf_hdr_write,
+      [HtsFile, BcfHdr],
+      :int
+
+    attach_function \
+      :vcf_parse,
+      [KString, BcfHdr, Bcf1],
+      :int
+
+    attach_function \
+      :vcf_open_mode,
+      %i[string string string],
+      :int
+
+    attach_function \
+      :vcf_format,
+      [BcfHdr, Bcf1, KString],
+      :int
+
+    attach_function \
+      :bcf_read,
+      [HtsFile, BcfHdr, Bcf1],
+      :int
+
+    attach_function \
+      :bcf_unpack,
+      [Bcf1, :int],
+      :int
+
+    attach_function \
+      :bcf_dup,
+      [Bcf1],
+      Bcf1.by_ref
+
+    attach_function \
+      :bcf_copy,
+      [Bcf1, Bcf1],
+      Bcf1.by_ref
+
+    attach_function \
+      :bcf_write,
+      [HtsFile, BcfHdr, Bcf1],
+      :int
+
+    attach_function \
+      :vcf_hdr_read,
+      [HtsFile],
+      BcfHdr.by_ref
+
+    attach_function \
+      :vcf_hdr_write,
+      [HtsFile, BcfHdr],
+      :int
+
+    attach_function \
+      :vcf_read,
+      [HtsFile, BcfHdr, Bcf1],
+      :int
+
+    attach_function \
+      :vcf_write,
+      [HtsFile, BcfHdr, Bcf1],
+      :int
+
+    attach_function \
+      :bcf_readrec,
+      [BGZF, :pointer, :pointer, :pointer, :hts_pos_t, :hts_pos_t],
+      :int
+
+    attach_function \
+      :vcf_write_line,
+      [HtsFile, KString],
+      :int
+
+    attach_function \
+      :bcf_hdr_dup,
+      [BcfHdr],
+      BcfHdr.by_ref
+
+    attach_function \
+      :bcf_hdr_merge,
+      [BcfHdr, BcfHdr],
+      BcfHdr.by_ref
+
+    attach_function \
+      :bcf_hdr_add_sample,
+      [BcfHdr, :string],
+      :int
+
+    attach_function \
+      :bcf_hdr_set,
+      [BcfHdr, :string],
+      :int
+
+    attach_function \
+      :bcf_hdr_format,
+      [BcfHdr, :int, KString],
+      :int
+
+    attach_function \
+      :bcf_hdr_fmt_text,
+      [BcfHdr, :int, :pointer],
+      :string
+
+    attach_function \
+      :bcf_hdr_append,
+      [BcfHdr, :string],
+      :int
+
+    attach_function \
+      :bcf_hdr_printf,
+      [BcfHdr, :string, :varargs],
+      :int
+
+    attach_function \
+      :bcf_hdr_get_version,
+      [BcfHdr],
+      :string
+
+    attach_function \
+      :bcf_hdr_set_version,
+      [BcfHdr, :string],
+      :int
+
+    attach_function \
+      :bcf_hdr_remove,
+      [BcfHdr, :int, :string],
+      :void
+
+    attach_function \
+      :bcf_hdr_subset,
+      [BcfHdr, :int, :pointer, :pointer],
+      BcfHdr.by_ref
+
+    attach_function \
+      :bcf_hdr_seqnames,
+      [BcfHdr, :pointer],
+      :pointer
+
+    attach_function \
+      :bcf_hdr_parse,
+      [BcfHdr, :string],
+      :int
+
+    attach_function \
+      :bcf_hdr_sync,
+      [BcfHdr],
+      :int
+
+    attach_function \
+      :bcf_hdr_parse_line,
+      [BcfHdr, :string, :pointer],
+      BcfHrec.by_ref
+
+    attach_function \
+      :bcf_hrec_format,
+      [BcfHrec, KString],
+      :int
+
+    attach_function \
+      :bcf_hdr_add_hrec,
+      [BcfHdr, BcfHrec],
+      :int
+
+    attach_function \
+      :bcf_hdr_get_hrec,
+      [BcfHdr, :int, :string, :string, :string],
+      BcfHrec.by_ref
+
+    attach_function \
+      :bcf_hrec_dup,
+      [BcfHrec],
+      BcfHrec.by_ref
+
+    attach_function \
+      :bcf_hrec_add_key,
+      [BcfHrec, :string, :size_t],
+      :int
+
+    attach_function \
+      :bcf_hrec_set_val,
+      [BcfHrec, :int, :string, :size_t, :int],
+      :int
+
+    attach_function \
+      :bcf_hrec_find_key,
+      [BcfHrec, :string],
+      :int
+
+    attach_function \
+      :hrec_add_idx,
+      [BcfHrec, :int],
+      :int
+
+    attach_function \
+      :bcf_hrec_destroy,
+      [BcfHrec],
+      :void
+
+    attach_function \
+      :bcf_subset,
+      [BcfHdr, Bcf1, :int, :pointer],
+      :int
+
+    attach_function \
+      :bcf_translate,
+      [BcfHdr, BcfHdr, Bcf1],
+      :int
+
+    attach_function \
+      :bcf_get_variant_types,
+      [Bcf1],
+      :int
+
+    attach_function \
+      :bcf_get_variant_type,
+      [Bcf1, :int],
+      :int
+
+    attach_function \
+      :bcf_is_snp,
+      [Bcf1],
+      :int
+
+    attach_function \
+      :bcf_update_filter,
+      [BcfHdr, Bcf1, :pointer, :int],
+      :int
+
+    attach_function \
+      :bcf_add_filter,
+      [BcfHdr, Bcf1, :int],
+      :int
+
+    attach_function \
+      :bcf_remove_filter,
+      [BcfHdr, Bcf1, :int, :int],
+      :int
+
+    attach_function \
+      :bcf_has_filter,
+      [BcfHdr, Bcf1, :string],
+      :int
+
+    attach_function \
+      :bcf_update_alleles,
+      [BcfHdr, Bcf1, :pointer, :int],
+      :int
+
+    attach_function \
+      :bcf_update_alleles_str,
+      [BcfHdr, Bcf1, :string],
+      :int
+
+    attach_function \
+      :bcf_update_id,
+      [BcfHdr, Bcf1, :string],
+      :int
+
+    attach_function \
+      :bcf_add_id,
+      [BcfHdr, Bcf1, :string],
+      :int
+
+    attach_function \
+      :bcf_update_info,
+      [BcfHdr, Bcf1, :string, :pointer, :int, :int],
+      :int
+
+    attach_function \
+      :bcf_update_format_string,
+      [BcfHdr, Bcf1, :string, :pointer, :int],
+      :int
+
+    attach_function \
+      :bcf_update_format,
+      [BcfHdr, Bcf1, :string, :pointer, :int, :int],
+      :int
+
+    attach_function \
+      :bcf_get_fmt,
+      [BcfHdr, Bcf1, :string],
+      BcfFmt.by_ref
+
+    attach_function \
+      :bcf_get_info,
+      [BcfHdr, Bcf1, :string],
+      BcfInfo.by_ref
+
+    attach_function \
+      :bcf_get_fmt_id,
+      [Bcf1, :int],
+      BcfFmt.by_ref
+
+    attach_function \
+      :bcf_get_info_id,
+      [Bcf1, :int],
+      BcfInfo.by_ref
+
+    attach_function \
+      :bcf_get_info_values,
+      [BcfHdr, Bcf1, :string, :pointer, :pointer, :int],
+      :int
+
+    attach_function \
+      :bcf_get_format_string,
+      [BcfHdr, Bcf1, :string, :pointer, :pointer],
+      :int
+
+    attach_function \
+      :bcf_get_format_values,
+      [BcfHdr, Bcf1, :string, :pointer, :pointer, :int],
+      :int
+
+    attach_function \
+      :bcf_hdr_id2int,
+      [BcfHdr, :int, :string],
+      :int
+
+    attach_function \
+      :bcf_fmt_array,
+      [KString, :int, :int, :pointer],
+      :int
+
+    attach_function \
+      :bcf_fmt_sized_array,
+      [KString, :pointer],
+      :uint8_t
+
+    attach_function \
+      :bcf_enc_vchar,
+      [KString, :int, :string],
+      :int
+
+    attach_function \
+      :bcf_enc_vint,
+      [KString, :int, :pointer, :int],
+      :int
+
+    attach_function \
+      :bcf_enc_vfloat,
+      [KString, :int, :pointer],
+      :int
+
+    attach_function \
+      :bcf_index_load2,
+      %i[string string],
+      HtsIdx.by_ref
+
+    attach_function \
+      :bcf_index_load3,
+      %i[string string int],
+      HtsIdx.by_ref
+
+    attach_function \
+      :bcf_index_build,
+      %i[string int],
+      :int
+
+    attach_function \
+      :bcf_index_build2,
+      %i[string string int],
+      :int
+
+    attach_function \
+      :bcf_index_build3,
+      %i[string string int int],
+      :int
+
+    attach_function \
+      :bcf_idx_init,
+      [HtsFile, BcfHdr, :int, :string],
+      :int
+
+    attach_function \
+      :bcf_idx_save,
+      [HtsFile],
+      :int
+  end
+end

data/lib/hts/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module HTS
-  VERSION = "0.0.5"
+  VERSION = "0.0.6"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: htslib
 version: !ruby/object:Gem::Version
-  version: 0.0.5
+  version: 0.0.6
 platform: ruby
 authors:
 - kojix2
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2021-12-26 00:00:00.000000000 Z
+date: 2022-01-03 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -122,7 +122,7 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
-description: 
+description:
 email:
 - 2xijok@gmail.com
 executables: []
@@ -152,8 +152,10 @@ files:
 - lib/hts/libhts/hts.rb
 - lib/hts/libhts/kfunc.rb
 - lib/hts/libhts/sam.rb
+- lib/hts/libhts/sam_funcs.rb
 - lib/hts/libhts/tbx.rb
 - lib/hts/libhts/vcf.rb
+- lib/hts/libhts/vcf_funcs.rb
 - lib/hts/tabix.rb
 - lib/hts/version.rb
 - lib/htslib.rb
@@ -161,7 +163,7 @@ homepage: https://github.com/kojix2/ruby-htslib
 licenses:
 - MIT
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -177,7 +179,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubygems_version: 3.3.3
-signing_key: 
+signing_key:
 specification_version: 4
 summary: HTSlib bindings for Ruby
 test_files: []