RubyGems - minimap2 - Versions diffs - 0.2.21 → 0.2.22.0 - Mend

minimap2 0.2.21 → 0.2.22.0

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Files changed (6) hide show

checksums.yaml +4 -4
data/lib/minimap2.rb +33 -17
data/lib/minimap2/ffi/constants.rb +57 -42
data/lib/minimap2/version.rb +2 -2
data/vendor/libminimap2.so +0 -0
metadata +17 -3

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data/lib/minimap2.rb CHANGED Viewed

@@ -34,27 +34,31 @@ module Minimap2
   # methods from mappy
   class << self
+    # Set verbosity level.
+    # @param [Integer] level
+    def verbose(level = -1)
+      FFI.mm_verbose_level(level)
+    end
     # Read fasta/fastq file.
     # @param [String] file_path
-    # @param [Boolean] read_comment If false or nil, the comment will not be read.
+    # @param [Boolean] comment If True, the comment will be read.
     # @yield [name, seq, qual, comment]
-    # Note: You can also use a generic library such as BioRuby instead of this method.
+    # @return [Enumerator] enum Retrun Enumerator if not block given.
+    # Note: You can BioRuby instead of this method.
-    def fastx_read(file_path, read_comment = false)
+    def fastx_read(file_path, comment: false, &block)
       path = File.expand_path(file_path)
       ks = FFI.mm_fastx_open(path)
-      while FFI.kseq_read(ks) >= 0
-        qual = ks[:qual][:s] if (ks[:qual][:l]).positive?
-        name = ks[:name][:s]
-        seq  = ks[:seq][:s]
-        if read_comment
-          comment = ks[:comment][:s] if (ks[:comment][:l]).positive?
-          yield [name, seq, qual, comment]
-        else
-          yield [name, seq, qual]
+      if block_given?
+        fastx_each(ks, comment, &block)
+      else
+        Enumerator.new do |y|
+          # rewind not work
+          fastx_each(ks, comment) { |r| y << r }
         end
       end
-      FFI.mm_fastx_close(ks)
     end
     # Reverse complement sequence.
@@ -68,11 +72,23 @@ module Minimap2
       FFI.mappy_revcomp(l, bseq)
     end
-    # Set verbosity level.
-    # @param [Integer] level
+    private
-    def verbose(level = -1)
-      FFI.mm_verbose_level(level)
+    def fastx_each(ks, comment)
+      yield fastx_next(ks, comment) while FFI.kseq_read(ks) >= 0
+      FFI.mm_fastx_close(ks)
+    end
+    def fastx_next(ks, read_comment)
+      qual = ks[:qual][:s] if (ks[:qual][:l]).positive?
+      name = ks[:name][:s]
+      seq  = ks[:seq][:s]
+      if read_comment
+        comment = ks[:comment][:s] if (ks[:comment][:l]).positive?
+        [name, seq, qual, comment]
+      else
+        [name, seq, qual]
+      end
     end
   end
 end

data/lib/minimap2/ffi/constants.rb CHANGED Viewed

@@ -3,48 +3,60 @@
 module Minimap2
   module FFI
     # flags
-    NO_DIAG        = 0x001 # no exact diagonal hit
-    NO_DUAL        = 0x002 # skip pairs where query name is lexicographically larger than target name
-    CIGAR          = 0x004
-    OUT_SAM        = 0x008
-    NO_QUAL        = 0x010
-    OUT_CG         = 0x020
-    OUT_CS         = 0x040
-    SPLICE         = 0x080 # splice mode
-    SPLICE_FOR     = 0x100 # match GT-AG
-    SPLICE_REV     = 0x200 # match CT-AC, the reverse complement of GT-AG
-    NO_LJOIN       = 0x400
-    OUT_CS_LONG    = 0x800
-    SR             = 0x1000
-    FRAG_MODE      = 0x2000
-    NO_PRINT_2ND   = 0x4000
-    TWO_IO_THREADS = 0x8000 # Translator's Note. MM_F_2_IO_THREADS. Constants starting with numbers cannot be defined.
-    LONG_CIGAR     = 0x10000
-    INDEPEND_SEG   = 0x20000
-    SPLICE_FLANK   = 0x40000
-    SOFTCLIP       = 0x80000
-    FOR_ONLY       = 0x100000
-    REV_ONLY       = 0x200000
-    HEAP_SORT      = 0x400000
-    ALL_CHAINS     = 0x800000
-    OUT_MD         = 0x1000000
-    COPY_COMMENT   = 0x2000000
-    EQX            = 0x4000000 # use =/X instead of M
-    PAF_NO_HIT     = 0x8000000 # output unmapped reads to PAF
-    NO_END_FLT     = 0x10000000
-    HARD_MLEVEL    = 0x20000000
-    SAM_HIT_ONLY   = 0x40000000
-    RMQ            = 0x80000000 # LL
-    HPC            = 0x1
-    NO_SEQ         = 0x2
-    NO_NAME        = 0x4
-    IDX_MAGIC      = "MMI\2"
-    MAX_SEG        = 255
-    CIGAR_STR      = 'MIDNSHP=XB'
+    NO_DIAG          = 0x001 # no exact diagonal hit
+    NO_DUAL          = 0x002 # skip pairs where query name is lexicographically larger than target name
+    CIGAR            = 0x004
+    OUT_SAM          = 0x008
+    NO_QUAL          = 0x010
+    OUT_CG           = 0x020
+    OUT_CS           = 0x040
+    SPLICE           = 0x080 # splice mode
+    SPLICE_FOR       = 0x100 # match GT-AG
+    SPLICE_REV       = 0x200 # match CT-AC, the reverse complement of GT-AG
+    NO_LJOIN         = 0x400
+    OUT_CS_LONG      = 0x800
+    SR               = 0x1000
+    FRAG_MODE        = 0x2000
+    NO_PRINT_2ND     = 0x4000
+    TWO_IO_THREADS   = 0x8000 # Translator's Note. MM_F_2_IO_THREADS. Constants starting with numbers cannot be defined.
+    LONG_CIGAR       = 0x10000
+    INDEPEND_SEG     = 0x20000
+    SPLICE_FLANK     = 0x40000
+    SOFTCLIP         = 0x80000
+    FOR_ONLY         = 0x100000
+    REV_ONLY         = 0x200000
+    HEAP_SORT        = 0x400000
+    ALL_CHAINS       = 0x800000
+    OUT_MD           = 0x1000000
+    COPY_COMMENT     = 0x2000000
+    EQX              = 0x4000000 # use =/X instead of M
+    PAF_NO_HIT       = 0x8000000 # output unmapped reads to PAF
+    NO_END_FLT       = 0x10000000
+    HARD_MLEVEL      = 0x20000000
+    SAM_HIT_ONLY     = 0x40000000
+    RMQ              = 0x80000000  # LL
+    QSTRAND          = 0x100000000 # LL
+    NO_INV           = 0x200000000
+    HPC              = 0x1
+    NO_SEQ           = 0x2
+    NO_NAME          = 0x4
+    IDX_MAGIC        = "MMI\2"
+    MAX_SEG          = 255
+    CIGAR_MATCH      = 0
+    CIGAR_INS        = 1
+    CIGAR_DEL        = 2
+    CIGAR_N_SKIP     = 3
+    CIGAR_SOFTCLIP   = 4
+    CIGAR_HARDCLIP   = 5
+    CIGAR_PADDING    = 6
+    CIGAR_EQ_MATCH   = 7
+    CIGAR_X_MISMATCH = 8
+    CIGAR_STR        = 'MIDNSHP=XB'
     # emulate 128-bit integers
     class MM128 < ::FFI::Struct
@@ -115,6 +127,8 @@ module Minimap2
         :anchor_ext_len,       :int,
         :anchor_ext_shift,     :int,
         :max_clip_ratio,       :float,   # drop an alignment if BOTH ends are clipped above this ratio
+        :rank_min_len,         :int,
+        :rank_frac,            :float,
         :pe_ori,               :int,
         :pe_bonus,             :int,
         :mid_occ_frac,         :float,   # only used by mm_mapopt_update(); see below
@@ -123,6 +137,7 @@ module Minimap2
         :max_occ,              :int32_t,
         :mini_batch_size,      :int64_t, # size of a batch of query bases to process in parallel
         :max_sw_mat,           :int64_t,
+        :cap_kalloc,           :int64_t,
         :split_prefix,         :string
     end

data/lib/minimap2/version.rb CHANGED Viewed

@@ -1,6 +1,6 @@
 # frozen_string_literal: true
 module Minimap2
-  # Minimap2-2.21 (r1071).
-  VERSION = '0.2.21'
+  # Minimap2-2.22 (r1101)
+  VERSION = '0.2.22.0'
 end

data/vendor/libminimap2.so CHANGED Viewed

Binary file

metadata CHANGED Viewed

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: minimap2
 version: !ruby/object:Gem::Version
-  version: 0.2.21
+  version: 0.2.22.0
 platform: ruby
 authors:
 - kojix2
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2021-07-06 00:00:00.000000000 Z
+date: 2021-08-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -38,6 +38,20 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
+- !ruby/object:Gem::Dependency
+  name: irb
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: minitest
   requirement: !ruby/object:Gem::Requirement
@@ -132,7 +146,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.2.15
+rubygems_version: 3.2.22
 signing_key:
 specification_version: 4
 summary: minimap2