htslib 0.0.0.pre → 0.0.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/README.md

@@ -1,6 +1,8 @@
 # HTSlib
 
+[![Gem Version](https://badge.fury.io/rb/htslib.svg)](https://badge.fury.io/rb/htslib)
 ![CI](https://github.com/kojix2/ruby-htslib/workflows/CI/badge.svg?branch=master)
+[![The MIT License](https://img.shields.io/badge/license-MIT-blue.svg)](LICENSE.txt)
 
 :apple: Feel free to fork it out if you can develop it! 
 

data/lib/hts/bam.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 # Create a skeleton using hts-python as a reference.
 # https://github.com/quinlan-lab/hts-python
 

data/lib/hts/fai.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 # Create a skeleton using hts-python as a reference.
 # https://github.com/quinlan-lab/hts-python
 

data/lib/hts/ffi.rb

@@ -29,3 +29,4 @@ require_relative 'ffi/hts'
 require_relative 'ffi/sam'
 require_relative 'ffi/kfunc'
 require_relative 'ffi/tbx'
+require_relative 'ffi/vcf'

data/lib/hts/ffi/bgzf.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 # BGZF
 module HTS
   module FFI

data/lib/hts/ffi/faidx.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 module HTS
   module FFI
     # Build index for a FASTA or FASTQ or bgzip-compressed FASTA or FASTQ file.

data/lib/hts/ffi/hfile.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 module HTS
   module FFI
     # Open the named file or URL as a stream

data/lib/hts/ffi/hts.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 module HTS
   module FFI
     # hts_expand

data/lib/hts/ffi/kfunc.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 module HTS
   module FFI
     # Log gamma function

data/lib/hts/ffi/sam.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 module HTS
   module FFI
     # macros

data/lib/hts/ffi/struct.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 # This should be removed if you get the better way...
 module FFI
   class Struct

data/lib/hts/ffi/tbx.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 module HTS
   module FFI
     attach_function \

data/lib/hts/ffi/vcf.rb

@@ -0,0 +1,430 @@
+# frozen_string_literal: true
+
+module HTS
+  module FFI
+    attach_function \
+      :bcf_hdr_init,
+      [:string],
+      BcfHdr.by_ref
+
+    attach_function \
+      :bcf_hdr_destroy,
+      [BcfHdr],
+      :void
+
+    attach_function \
+      :bcf_init,
+      [:void],
+      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/ffi_constants.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 module HTS
   module FFI
     typedef :pointer, :HFILE
@@ -266,8 +268,8 @@ module HTS
     BAM_CDIFF      = 8
     BAM_CBACK      = 9
 
-    BAM_CIGAR_STR = 'MIDNSHP=XB'.freeze
-    BAM_CIGAR_STR_PADDED = 'MIDNSHP=XB??????'.freeze
+    BAM_CIGAR_STR = 'MIDNSHP=XB'
+    BAM_CIGAR_STR_PADDED = 'MIDNSHP=XB??????'
     BAM_CIGAR_SHIFT = 4
     BAM_CIGAR_MASK  = 0xf
     BAM_CIGAR_TYPE  = 0x3C1A7

data/lib/hts/tbx.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 # Create a skeleton using hts-python as a reference.
 # https://github.com/quinlan-lab/hts-python
 

data/lib/hts/vcf.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 # Create a skeleton using hts-python as a reference.
 # https://github.com/quinlan-lab/hts-python
 

data/lib/hts/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module HTS
-  VERSION = '0.0.0.pre'
+  VERSION = '0.0.0'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: htslib
 version: !ruby/object:Gem::Version
-  version: 0.0.0.pre
+  version: 0.0.0
 platform: ruby
 authors:
 - kojix2
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-08-20 00:00:00.000000000 Z
+date: 2020-10-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -114,6 +114,7 @@ files:
 - lib/hts/ffi/sam.rb
 - lib/hts/ffi/struct.rb
 - lib/hts/ffi/tbx.rb
+- lib/hts/ffi/vcf.rb
 - lib/hts/ffi_constants.rb
 - lib/hts/tbx.rb
 - lib/hts/vcf.rb
@@ -134,11 +135,11 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '2.4'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">"
+  - - ">="
     - !ruby/object:Gem::Version
-      version: 1.3.1
+      version: '0'
 requirements: []
-rubygems_version: 3.1.2
+rubygems_version: 3.1.4
 signing_key: 
 specification_version: 4
 summary: HTSlib bindings for Ruby