htslib 0.0.10 → 0.2.1
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 +4 -4
- data/README.md +46 -27
- data/lib/hts/bam/aux.rb +40 -0
- data/lib/hts/bam/cigar.rb +5 -10
- data/lib/hts/bam/flag.rb +26 -57
- data/lib/hts/bam/header.rb +2 -4
- data/lib/hts/bam/record.rb +94 -47
- data/lib/hts/bam.rb +125 -37
- data/lib/hts/bcf/format.rb +84 -13
- data/lib/hts/bcf/header.rb +1 -0
- data/lib/hts/bcf/header_record.rb +11 -0
- data/lib/hts/bcf/info.rb +57 -31
- data/lib/hts/bcf/record.rb +63 -35
- data/lib/hts/bcf.rb +204 -30
- data/lib/hts/faidx.rb +62 -24
- data/lib/hts/ffi_ext/pointer.rb +18 -0
- data/lib/hts/hts.rb +71 -6
- data/lib/hts/libhts/bgzf.rb +5 -5
- data/lib/hts/libhts/constants.rb +45 -23
- data/lib/hts/libhts/cram.rb +295 -292
- data/lib/hts/libhts/hfile.rb +29 -11
- data/lib/hts/libhts/hts.rb +158 -25
- data/lib/hts/libhts/sam.rb +683 -94
- data/lib/hts/libhts/sam_funcs.rb +131 -588
- data/lib/hts/libhts/vcf.rb +433 -220
- data/lib/hts/libhts/vcf_funcs.rb +258 -424
- data/lib/hts/libhts.rb +5 -0
- data/lib/hts/{tabix.rb → tbx.rb} +6 -14
- data/lib/hts/version.rb +1 -1
- data/lib/htslib.rb +1 -1
- data/vendor/libhts.dylib +0 -0
- metadata +12 -8
data/lib/hts/libhts/constants.rb
CHANGED
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@@ -1,6 +1,7 @@
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# frozen_string_literal: true
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module HTS
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+
# Module for working with C HTSlib.
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module LibHTS
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typedef :int64, :hts_pos_t
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typedef :pointer, :bam_plp_auto_f
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@@ -24,9 +25,9 @@ module HTS
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:f, :pointer # kstream_t
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end
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-
#
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# HFile
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-
class
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class HFile < FFI::BitStruct
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layout \
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:buffer, :string,
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:begin, :string,
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@@ -36,7 +37,7 @@ module HTS
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:offset, :size_t,
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:_flags, :uint,
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:has_errno, :int
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-
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+
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bit_fields :_flags,
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:at_eof, 1,
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:mobile, 1,
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@@ -56,7 +57,7 @@ module HTS
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:uncompressed_block, :pointer,
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:compressed_block, :pointer,
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:cache, :pointer,
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:fp,
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:fp, HFile.ptr,
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:mt, :pointer,
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:idx, :pointer,
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:idx_build_otf, :int,
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@@ -189,6 +190,16 @@ module HTS
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)
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end
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class HtsReglist < FFI::Struct
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layout \
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:reg, :string,
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:intervals, :pointer, # hts_pair_pos_t
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:tid, :int,
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:count, :uint32_t,
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:min_beg, :hts_pos_t,
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:max_end, :hts_pos_t
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end
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+
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# HtsFile
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class SamHdr < FFI::Struct
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layout \
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@@ -217,7 +228,7 @@ module HTS
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union_layout(
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:bgzf, BGZF.ptr,
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:cram, :pointer, # cram_fd
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:hfile,
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:hfile, HFile.ptr
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),
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:state, :pointer,
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:format, HtsFormat,
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@@ -263,7 +274,7 @@ module HTS
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:n_reg, :int,
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:beg, :int64,
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:end, :int64,
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:reg_list, :pointer,
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:reg_list, :pointer, # HtsReglist.ptr,
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:curr_tid, :int,
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:curr_reg, :int,
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:curr_intv, :int,
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@@ -392,6 +403,7 @@ module HTS
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:n, :int
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end
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+
# Complete textual representation of a header line
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class BcfHrec < FFI::Struct
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layout \
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:type, :int,
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@@ -402,21 +414,6 @@ module HTS
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:vals, :pointer
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end
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-
class BcfFmt < FFI::BitStruct
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layout \
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:id, :int,
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:n, :int,
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:size, :int,
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:type, :int,
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:p, :pointer, # uint8_t
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:p_len, :uint32,
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:_p_off_free, :uint32 # bit_fields
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-
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bit_fields :_p_off_free,
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:p_off, 31,
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:p_free, 1
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-
end
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-
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class BcfInfo < FFI::BitStruct
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layout \
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:key, :int,
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@@ -466,6 +463,21 @@ module HTS
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:m, [:int, 3]
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end
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class BcfFmt < FFI::BitStruct
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layout \
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:id, :int,
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:n, :int,
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:size, :int,
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:type, :int,
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:p, :pointer, # uint8_t
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:p_len, :uint32,
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:_p_off_free, :uint32 # bit_fields
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bit_fields :_p_off_free,
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:p_off, 31,
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:p_free, 1
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end
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class BcfDec < FFI::Struct
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layout \
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:m_fmt, :int,
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@@ -479,8 +491,8 @@ module HTS
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:id, :string,
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:als, :pointer, # (\\0-separated string)
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:allele, :pointer,
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:info, :pointer, # BcfInfo.ptr,
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:fmt, BcfFmt.ptr,
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:info, :pointer, # array of BcfInfo.ptr,
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:fmt, :pointer, # array of BcfFmt.ptr,
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:var, BcfVariant.ptr,
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:n_var, :int,
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:var_type, :int,
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@@ -516,5 +528,15 @@ module HTS
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LibHTS.bcf_destroy(ptr) unless ptr.null?
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end
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end
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CramContentType = enum(
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:ct_error, -1,
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:file_header, 0,
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:compression_header, 1,
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:mapped_slice, 2,
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:unmapped_slice, 3, # cram v1.0 only
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:external, 4,
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:core, 5
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)
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end
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end
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