htslib 0.0.0.pre → 0.0.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
checksums.yaml CHANGED
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data/README.md CHANGED
@@ -1,6 +1,8 @@
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  # HTSlib
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+ [![Gem Version](https://badge.fury.io/rb/htslib.svg)](https://badge.fury.io/rb/htslib)
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  ![CI](https://github.com/kojix2/ruby-htslib/workflows/CI/badge.svg?branch=master)
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+ [![The MIT License](https://img.shields.io/badge/license-MIT-blue.svg)](LICENSE.txt)
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  :apple: Feel free to fork it out if you can develop it!
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@@ -1,3 +1,5 @@
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+ # frozen_string_literal: true
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+
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  # Create a skeleton using hts-python as a reference.
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  # https://github.com/quinlan-lab/hts-python
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@@ -1,3 +1,5 @@
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+ # frozen_string_literal: true
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+
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  # Create a skeleton using hts-python as a reference.
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  # https://github.com/quinlan-lab/hts-python
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@@ -29,3 +29,4 @@ require_relative 'ffi/hts'
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  require_relative 'ffi/sam'
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  require_relative 'ffi/kfunc'
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  require_relative 'ffi/tbx'
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+ require_relative 'ffi/vcf'
@@ -1,3 +1,5 @@
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+ # frozen_string_literal: true
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+
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  # BGZF
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  module HTS
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  module FFI
@@ -1,3 +1,5 @@
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+ # frozen_string_literal: true
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+
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  module HTS
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  module FFI
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  # Build index for a FASTA or FASTQ or bgzip-compressed FASTA or FASTQ file.
@@ -1,3 +1,5 @@
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+ # frozen_string_literal: true
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+
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  module HTS
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  module FFI
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  # Open the named file or URL as a stream
@@ -1,3 +1,5 @@
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+ # frozen_string_literal: true
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+
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  module HTS
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  module FFI
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  # hts_expand
@@ -1,3 +1,5 @@
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+ # frozen_string_literal: true
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+
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  module HTS
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  module FFI
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  # Log gamma function
@@ -1,3 +1,5 @@
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+ # frozen_string_literal: true
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+
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  module HTS
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  module FFI
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  # macros
@@ -1,3 +1,5 @@
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+ # frozen_string_literal: true
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+
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  # This should be removed if you get the better way...
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  module FFI
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  class Struct
@@ -1,3 +1,5 @@
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+ # frozen_string_literal: true
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+
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  module HTS
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  module FFI
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  attach_function \
@@ -0,0 +1,430 @@
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+ # frozen_string_literal: true
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+
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+ module HTS
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+ module FFI
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+ attach_function \
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+ :bcf_hdr_init,
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+ [:string],
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+ BcfHdr.by_ref
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+
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+ attach_function \
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+ :bcf_hdr_destroy,
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+ [BcfHdr],
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+ :void
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+
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+ attach_function \
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+ :bcf_init,
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+ [:void],
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+ Bcf1.by_ref
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+
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+ attach_function \
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+ :bcf_destroy,
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+ [Bcf1],
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+ :void
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+
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+ attach_function \
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+ :bcf_empty,
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+ [Bcf1],
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+ :void
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+
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+ attach_function \
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+ :bcf_clear,
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+ [Bcf1],
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+ :void
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+
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+ attach_function \
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+ :bcf_hdr_read,
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+ [HtsFile],
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+ BcfHdr.by_ref
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+
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+ attach_function \
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+ :bcf_hdr_set_samples,
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+ [BcfHdr, :string, :int],
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+ :int
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+
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+ attach_function \
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+ :bcf_subset_format,
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+ [BcfHdr, Bcf1],
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+ :int
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+
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+ attach_function \
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+ :bcf_hdr_write,
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+ [HtsFile, BcfHdr],
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+ :int
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+
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+ attach_function \
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+ :vcf_parse,
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+ [Kstring, BcfHdr, Bcf1],
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+ :int
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+
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+ attach_function \
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+ :vcf_open_mode,
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+ %i[string string string],
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+ :int
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+
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+ attach_function \
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+ :vcf_format,
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+ [BcfHdr, Bcf1, Kstring],
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+ :int
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+
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+ attach_function \
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+ :bcf_read,
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+ [HtsFile, BcfHdr, Bcf1],
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+ :int
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+
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+ attach_function \
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+ :bcf_unpack,
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+ [Bcf1, :int],
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+ :int
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+
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+ attach_function \
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+ :bcf_dup,
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+ [Bcf1],
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+ Bcf1.by_ref
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+
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+ attach_function \
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+ :bcf_copy,
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+ [Bcf1, Bcf1],
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+ Bcf1.by_ref
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+
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+ attach_function \
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+ :bcf_write,
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+ [HtsFile, BcfHdr, Bcf1],
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+ :int
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+
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+ attach_function \
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+ :vcf_hdr_read,
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+ [HtsFile],
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+ BcfHdr.by_ref
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+
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+ attach_function \
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+ :vcf_hdr_write,
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+ [HtsFile, BcfHdr],
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+ :int
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+
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+ attach_function \
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+ :vcf_read,
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+ [HtsFile, BcfHdr, Bcf1],
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+ :int
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+
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+ attach_function \
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+ :vcf_write,
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+ [HtsFile, BcfHdr, Bcf1],
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+ :int
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+
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+ attach_function \
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+ :bcf_readrec,
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+ [BGZF, :pointer, :pointer, :pointer, :hts_pos_t, :hts_pos_t],
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+ :int
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+
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+ attach_function \
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+ :vcf_write_line,
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+ [HtsFile, Kstring],
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+ :int
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+
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+ attach_function \
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+ :bcf_hdr_dup,
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+ [BcfHdr],
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+ BcfHdr.by_ref
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+
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+ attach_function \
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+ :bcf_hdr_merge,
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+ [BcfHdr, BcfHdr],
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+ BcfHdr.by_ref
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+
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+ attach_function \
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+ :bcf_hdr_add_sample,
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+ [BcfHdr, :string],
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+ :int
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+
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+ attach_function \
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+ :bcf_hdr_set,
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+ [BcfHdr, :string],
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+ :int
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+
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+ attach_function \
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+ :bcf_hdr_format,
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+ [BcfHdr, :int, Kstring],
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+ :int
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+
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+ attach_function \
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+ :bcf_hdr_fmt_text,
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+ [BcfHdr, :int, :pointer],
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+ :string
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+
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+ attach_function \
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+ :bcf_hdr_append,
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+ [BcfHdr, :string],
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+ :int
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+
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+ attach_function \
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+ :bcf_hdr_printf,
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+ [BcfHdr, :string, :varargs],
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+ :int
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+
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+ attach_function \
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+ :bcf_hdr_get_version,
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+ [BcfHdr],
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+ :string
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+
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+ attach_function \
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+ :bcf_hdr_set_version,
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+ [BcfHdr, :string],
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+ :int
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+
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+ attach_function \
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+ :bcf_hdr_remove,
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+ [BcfHdr, :int, :string],
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+ :void
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+
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+ attach_function \
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+ :bcf_hdr_subset,
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+ [BcfHdr, :int, :pointer, :pointer],
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+ BcfHdr.by_ref
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+
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+ attach_function \
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+ :bcf_hdr_seqnames,
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+ [BcfHdr, :pointer],
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+ :pointer
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+
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+ attach_function \
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+ :bcf_hdr_parse,
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+ [BcfHdr, :string],
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+ :int
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+
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+ attach_function \
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+ :bcf_hdr_sync,
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+ [BcfHdr],
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+ :int
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+
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+ attach_function \
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+ :bcf_hdr_parse_line,
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+ [BcfHdr, :string, :pointer],
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+ BcfHrec.by_ref
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+
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+ attach_function \
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+ :bcf_hrec_format,
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+ [BcfHrec, Kstring],
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+ :int
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+
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+ attach_function \
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+ :bcf_hdr_add_hrec,
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+ [BcfHdr, BcfHrec],
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+ :int
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+
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+ attach_function \
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+ :bcf_hdr_get_hrec,
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+ [BcfHdr, :int, :string, :string, :string],
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+ BcfHrec.by_ref
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+
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+ attach_function \
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+ :bcf_hrec_dup,
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+ [BcfHrec],
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+ BcfHrec.by_ref
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+
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+ attach_function \
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+ :bcf_hrec_add_key,
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+ [BcfHrec, :string, :size_t],
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+ :int
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+
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+ attach_function \
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+ :bcf_hrec_set_val,
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+ [BcfHrec, :int, :string, :size_t, :int],
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+ :int
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+
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+ attach_function \
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+ :bcf_hrec_find_key,
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+ [BcfHrec, :string],
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+ :int
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+
240
+ attach_function \
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+ :hrec_add_idx,
242
+ [BcfHrec, :int],
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+ :int
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+
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+ attach_function \
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+ :bcf_hrec_destroy,
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+ [BcfHrec],
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+ :void
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+
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+ attach_function \
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+ :bcf_subset,
252
+ [BcfHdr, Bcf1, :int, :pointer],
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+ :int
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+
255
+ attach_function \
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+ :bcf_translate,
257
+ [BcfHdr, BcfHdr, Bcf1],
258
+ :int
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+
260
+ attach_function \
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+ :bcf_get_variant_types,
262
+ [Bcf1],
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+ :int
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+
265
+ attach_function \
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+ :bcf_get_variant_type,
267
+ [Bcf1, :int],
268
+ :int
269
+
270
+ attach_function \
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+ :bcf_is_snp,
272
+ [Bcf1],
273
+ :int
274
+
275
+ attach_function \
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+ :bcf_update_filter,
277
+ [BcfHdr, Bcf1, :pointer, :int],
278
+ :int
279
+
280
+ attach_function \
281
+ :bcf_add_filter,
282
+ [BcfHdr, Bcf1, :int],
283
+ :int
284
+
285
+ attach_function \
286
+ :bcf_remove_filter,
287
+ [BcfHdr, Bcf1, :int, :int],
288
+ :int
289
+
290
+ attach_function \
291
+ :bcf_has_filter,
292
+ [BcfHdr, Bcf1, :string],
293
+ :int
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+
295
+ attach_function \
296
+ :bcf_update_alleles,
297
+ [BcfHdr, Bcf1, :pointer, :int],
298
+ :int
299
+
300
+ attach_function \
301
+ :bcf_update_alleles_str,
302
+ [BcfHdr, Bcf1, :string],
303
+ :int
304
+
305
+ attach_function \
306
+ :bcf_update_id,
307
+ [BcfHdr, Bcf1, :string],
308
+ :int
309
+
310
+ attach_function \
311
+ :bcf_add_id,
312
+ [BcfHdr, Bcf1, :string],
313
+ :int
314
+
315
+ attach_function \
316
+ :bcf_update_info,
317
+ [BcfHdr, Bcf1, :string, :pointer, :int, :int],
318
+ :int
319
+
320
+ attach_function \
321
+ :bcf_update_format_string,
322
+ [BcfHdr, Bcf1, :string, :pointer, :int],
323
+ :int
324
+
325
+ attach_function \
326
+ :bcf_update_format,
327
+ [BcfHdr, Bcf1, :string, :pointer, :int, :int],
328
+ :int
329
+
330
+ attach_function \
331
+ :bcf_get_fmt,
332
+ [BcfHdr, Bcf1, :string],
333
+ BcfFmt.by_ref
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+
335
+ attach_function \
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+ :bcf_get_info,
337
+ [BcfHdr, Bcf1, :string],
338
+ BcfInfo.by_ref
339
+
340
+ attach_function \
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+ :bcf_get_fmt_id,
342
+ [Bcf1, :int],
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+ BcfFmt.by_ref
344
+
345
+ attach_function \
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+ :bcf_get_info_id,
347
+ [Bcf1, :int],
348
+ BcfInfo.by_ref
349
+
350
+ attach_function \
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+ :bcf_get_info_values,
352
+ [BcfHdr, Bcf1, :string, :pointer, :pointer, :int],
353
+ :int
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+
355
+ attach_function \
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+ :bcf_get_format_string,
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+ [BcfHdr, Bcf1, :string, :pointer, :pointer],
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+ :int
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+
360
+ attach_function \
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+ :bcf_get_format_values,
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+ [BcfHdr, Bcf1, :string, :pointer, :pointer, :int],
363
+ :int
364
+
365
+ attach_function \
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+ :bcf_hdr_id2int,
367
+ [BcfHdr, :int, :string],
368
+ :int
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+
370
+ attach_function \
371
+ :bcf_fmt_array,
372
+ [Kstring, :int, :int, :pointer],
373
+ :int
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+
375
+ attach_function \
376
+ :bcf_fmt_sized_array,
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+ [Kstring, :pointer],
378
+ :uint8_t
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+
380
+ attach_function \
381
+ :bcf_enc_vchar,
382
+ [Kstring, :int, :string],
383
+ :int
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+
385
+ attach_function \
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+ :bcf_enc_vint,
387
+ [Kstring, :int, :pointer, :int],
388
+ :int
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+
390
+ attach_function \
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+ :bcf_enc_vfloat,
392
+ [Kstring, :int, :pointer],
393
+ :int
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+
395
+ attach_function \
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+ :bcf_index_load2,
397
+ %i[string string],
398
+ HtsIdx.by_ref
399
+
400
+ attach_function \
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+ :bcf_index_load3,
402
+ %i[string string int],
403
+ HtsIdx.by_ref
404
+
405
+ attach_function \
406
+ :bcf_index_build,
407
+ %i[string int],
408
+ :int
409
+
410
+ attach_function \
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+ :bcf_index_build2,
412
+ %i[string string int],
413
+ :int
414
+
415
+ attach_function \
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+ :bcf_index_build3,
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+ %i[string string int int],
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+ :int
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+
420
+ attach_function \
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+ :bcf_idx_init,
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+ [HtsFile, BcfHdr, :int, :string],
423
+ :int
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+
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+ attach_function \
426
+ :bcf_idx_save,
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+ [HtsFile],
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+ :int
429
+ end
430
+ end
@@ -1,3 +1,5 @@
1
+ # frozen_string_literal: true
2
+
1
3
  module HTS
2
4
  module FFI
3
5
  typedef :pointer, :HFILE
@@ -266,8 +268,8 @@ module HTS
266
268
  BAM_CDIFF = 8
267
269
  BAM_CBACK = 9
268
270
 
269
- BAM_CIGAR_STR = 'MIDNSHP=XB'.freeze
270
- BAM_CIGAR_STR_PADDED = 'MIDNSHP=XB??????'.freeze
271
+ BAM_CIGAR_STR = 'MIDNSHP=XB'
272
+ BAM_CIGAR_STR_PADDED = 'MIDNSHP=XB??????'
271
273
  BAM_CIGAR_SHIFT = 4
272
274
  BAM_CIGAR_MASK = 0xf
273
275
  BAM_CIGAR_TYPE = 0x3C1A7
@@ -1,3 +1,5 @@
1
+ # frozen_string_literal: true
2
+
1
3
  # Create a skeleton using hts-python as a reference.
2
4
  # https://github.com/quinlan-lab/hts-python
3
5
 
@@ -1,3 +1,5 @@
1
+ # frozen_string_literal: true
2
+
1
3
  # Create a skeleton using hts-python as a reference.
2
4
  # https://github.com/quinlan-lab/hts-python
3
5
 
@@ -1,5 +1,5 @@
1
1
  # frozen_string_literal: true
2
2
 
3
3
  module HTS
4
- VERSION = '0.0.0.pre'
4
+ VERSION = '0.0.0'
5
5
  end
metadata CHANGED
@@ -1,14 +1,14 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: htslib
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.0.0.pre
4
+ version: 0.0.0
5
5
  platform: ruby
6
6
  authors:
7
7
  - kojix2
8
8
  autorequire:
9
9
  bindir: bin
10
10
  cert_chain: []
11
- date: 2020-08-20 00:00:00.000000000 Z
11
+ date: 2020-10-21 00:00:00.000000000 Z
12
12
  dependencies:
13
13
  - !ruby/object:Gem::Dependency
14
14
  name: ffi
@@ -114,6 +114,7 @@ files:
114
114
  - lib/hts/ffi/sam.rb
115
115
  - lib/hts/ffi/struct.rb
116
116
  - lib/hts/ffi/tbx.rb
117
+ - lib/hts/ffi/vcf.rb
117
118
  - lib/hts/ffi_constants.rb
118
119
  - lib/hts/tbx.rb
119
120
  - lib/hts/vcf.rb
@@ -134,11 +135,11 @@ required_ruby_version: !ruby/object:Gem::Requirement
134
135
  version: '2.4'
135
136
  required_rubygems_version: !ruby/object:Gem::Requirement
136
137
  requirements:
137
- - - ">"
138
+ - - ">="
138
139
  - !ruby/object:Gem::Version
139
- version: 1.3.1
140
+ version: '0'
140
141
  requirements: []
141
- rubygems_version: 3.1.2
142
+ rubygems_version: 3.1.4
142
143
  signing_key:
143
144
  specification_version: 4
144
145
  summary: HTSlib bindings for Ruby