minibwa 0.0.0

data/lib/minibwa/options.rb

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+# frozen_string_literal: true
+
+module Minibwa
+  # Alignment parameters, a Ruby view of mb_opt_t.
+  #
+  # The class and all of its field accessors come from mb_options.c; this file
+  # reopens it for what reads better in Ruby -- keyword initialization,
+  # #to_h and #inspect, and rejecting an unknown preset name before it reaches
+  # mb_opt_preset().
+  #
+  # Presets are "sr", "adap" and "lr". Note that mb_opt_init() applies "adap",
+  # so a fresh Options is paired-end and adaptive by default.
+  #
+  # @!attribute [rw] flag
+  #   @return [Integer] raw bit flags.
+  # @!attribute [rw] min_len
+  #   @return [Integer] minimum seed length.
+  # @!attribute [rw] max_sub_occ
+  #   @return [Integer] maximum occurrence count for sub-seeds.
+  # @!attribute [rw] max_occ
+  #   @return [Integer] maximum occurrence count for seeds.
+  # @!attribute [rw] bw
+  #   @return [Integer] band width for dynamic programming.
+  # @!attribute [rw] bw_long
+  #   @return [Integer] band width for long alignments.
+  # @!attribute [rw] max_gap
+  #   @return [Integer] maximum gap size considered during chaining.
+  # @!attribute [rw] max_sr_len
+  #   @return [Integer] maximum short-read length.
+  # @!attribute [rw] max_chain_skip
+  #   @return [Integer] maximum skipped anchors during chaining.
+  # @!attribute [rw] max_chain_iter
+  #   @return [Integer] maximum chaining iterations.
+  # @!attribute [rw] min_chain_score
+  #   @return [Integer] minimum chaining score.
+  # @!attribute [rw] chain_gap_scale
+  #   @return [Float] gap penalty scale for chaining.
+  # @!attribute [rw] mask_level
+  #   @return [Float] masking level for secondary hits.
+  # @!attribute [rw] mask_len
+  #   @return [Integer] masking length threshold.
+  # @!attribute [rw] pri_ratio
+  #   @return [Float] primary-to-secondary score ratio.
+  # @!attribute [rw] best_n
+  #   @return [Integer] number of best hits retained.
+  # @!attribute [rw] a
+  #   @return [Integer] match score.
+  # @!attribute [rw] b
+  #   @return [Integer] mismatch penalty.
+  # @!attribute [rw] b_ts
+  #   @return [Integer] transition mismatch penalty.
+  # @!attribute [rw] b_ambi
+  #   @return [Integer] ambiguous-base mismatch penalty.
+  # @!attribute [rw] q
+  #   @return [Integer] gap-open penalty.
+  # @!attribute [rw] q2
+  #   @return [Integer] second gap-open penalty.
+  # @!attribute [rw] e
+  #   @return [Integer] gap-extension penalty.
+  # @!attribute [rw] e2
+  #   @return [Integer] second gap-extension penalty.
+  # @!attribute [rw] end_bonus
+  #   @return [Integer] alignment end bonus.
+  # @!attribute [rw] min_dp_max
+  #   @return [Integer] minimum dynamic-programming score.
+  # @!attribute [rw] zdrop
+  #   @return [Integer] Z-drop threshold.
+  # @!attribute [rw] zdrop_inv
+  #   @return [Integer] inversion Z-drop threshold.
+  # @!attribute [rw] min_ksw_len
+  #   @return [Integer] minimum length for Smith-Waterman alignment.
+  # @!attribute [rw] max_pe_ins
+  #   @return [Integer] maximum paired-end insert size.
+  # @!attribute [rw] max_rescue
+  #   @return [Integer] maximum rescue attempts.
+  # @!attribute [rw] pen_unpair
+  #   @return [Integer] unpaired alignment penalty.
+  # @!attribute [rw] pe_avg
+  #   @return [Integer] paired-end insert-size average.
+  # @!attribute [rw] pe_std
+  #   @return [Integer] paired-end insert-size standard deviation.
+  # @!attribute [rw] pe_lo
+  #   @return [Integer] paired-end lower insert-size bound.
+  # @!attribute [rw] pe_hi
+  #   @return [Integer] paired-end upper insert-size bound.
+  # @!attribute [rw] sb_len
+  #   @return [Integer] sequence batch length.
+  # @!attribute [rw] sb_seq
+  #   @return [Integer] sequence batch count.
+  # @!attribute [rw] n_thread
+  #   @return [Integer] number of threads for batch work.
+  # @!attribute [rw] out_n
+  #   @return [Integer] maximum number of output alignments.
+  # @!attribute [rw] out_s
+  #   @return [Float] minimum output score ratio.
+  # @!attribute [rw] seed
+  #   @return [Integer] random seed.
+  # @!attribute [rw] xa_max
+  #   @return [Integer] maximum XA tag hits.
+  # @!attribute [rw] mb_size
+  #   @return [Integer] mini-batch size.
+  # @!attribute [rw] max_mb_size
+  #   @return [Integer] maximum mini-batch size.
+  # @!attribute [rw] max_sw_mat
+  #   @return [Integer] maximum Smith-Waterman matrix size.
+  # @!attribute [rw] cap_kalloc
+  #   @return [Integer] kalloc capacity limit.
+  #
+  # @!method paf?
+  #   @return [Boolean] whether PAF output mode is enabled.
+  # @!method paf=(value)
+  #   @return [Object] value
+  # @!method no_unmap?
+  #   @return [Boolean] whether unmapped records are suppressed.
+  # @!method no_unmap=(value)
+  #   @return [Object] value
+  # @!method copy_comment?
+  #   @return [Boolean] whether FASTQ comments are copied.
+  # @!method copy_comment=(value)
+  #   @return [Object] value
+  # @!method pe?
+  #   @return [Boolean] whether paired-end mode is enabled.
+  # @!method pe=(value)
+  #   @return [Object] value
+  # @!method long_mode?
+  #   @return [Boolean] whether long-read mode is enabled.
+  # @!method long_mode=(value)
+  #   @return [Object] value
+  # @!method eqx?
+  #   @return [Boolean] whether CIGAR uses =/X operators.
+  # @!method eqx=(value)
+  #   @return [Object] value
+  # @!method no_kalloc?
+  #   @return [Boolean] whether kalloc is disabled.
+  # @!method no_kalloc=(value)
+  #   @return [Object] value
+  # @!method no_aln?
+  #   @return [Boolean] whether alignment is disabled.
+  # @!method no_aln=(value)
+  #   @return [Object] value
+  # @!method pe_predef?
+  #   @return [Boolean] whether paired-end bounds are predefined.
+  # @!method pe_predef=(value)
+  #   @return [Object] value
+  # @!method write_ds?
+  #   @return [Boolean] whether the DS tag is emitted.
+  # @!method write_ds=(value)
+  #   @return [Object] value
+  # @!method write_cs?
+  #   @return [Boolean] whether the CS tag is emitted.
+  # @!method write_cs=(value)
+  #   @return [Object] value
+  # @!method write_md?
+  #   @return [Boolean] whether the MD tag is emitted.
+  # @!method write_md=(value)
+  #   @return [Object] value
+  # @!method second_seq?
+  #   @return [Boolean] whether second-sequence output is enabled.
+  # @!method second_seq=(value)
+  #   @return [Object] value
+  # @!method supp_soft?
+  #   @return [Boolean] whether supplementary alignments use soft clipping.
+  # @!method supp_soft=(value)
+  #   @return [Object] value
+  # @!method adap?
+  #   @return [Boolean] whether adaptive mode is enabled.
+  # @!method adap=(value)
+  #   @return [Object] value
+  # @!method primary5?
+  #   @return [Boolean] whether primary alignment selection is 5-prime based.
+  # @!method primary5=(value)
+  #   @return [Object] value
+  # @!method no_pairing?
+  #   @return [Boolean] whether pairing is disabled.
+  # @!method no_pairing=(value)
+  #   @return [Object] value
+  # @!method meth?
+  #   @return [Boolean] whether methylation mode is enabled.
+  # @!method meth=(value)
+  #   @return [Object] value
+  class Options
+    # Supported preset names for {#preset}.
+    PRESETS = %w[sr adap lr].freeze
+
+    # Applies a named preset with validation.
+    #
+    #   opt.preset("sr")   # => true
+    #   opt.preset("bad")  # raises ArgumentError
+    def preset(name)
+      unless PRESETS.include?(name.to_s)
+        raise ArgumentError, "unknown preset: #{name.inspect}, expected one of #{PRESETS.inspect}"
+      end
+
+      preset!(name)
+    end
+
+    # Returns all field values as a Hash.
+    def to_h
+      {
+        flag: flag, min_len: min_len, max_sub_occ: max_sub_occ, max_occ: max_occ,
+        bw: bw, bw_long: bw_long, max_gap: max_gap, max_sr_len: max_sr_len,
+        max_chain_skip: max_chain_skip, max_chain_iter: max_chain_iter,
+        min_chain_score: min_chain_score, chain_gap_scale: chain_gap_scale,
+        mask_level: mask_level, mask_len: mask_len, pri_ratio: pri_ratio,
+        best_n: best_n, a: a, b: b, b_ts: b_ts, b_ambi: b_ambi,
+        q: q, q2: q2, e: e, e2: e2, end_bonus: end_bonus,
+        min_dp_max: min_dp_max, zdrop: zdrop, zdrop_inv: zdrop_inv,
+        min_ksw_len: min_ksw_len, max_pe_ins: max_pe_ins, max_rescue: max_rescue,
+        pen_unpair: pen_unpair, pe_avg: pe_avg, pe_std: pe_std,
+        pe_lo: pe_lo, pe_hi: pe_hi, sb_len: sb_len, sb_seq: sb_seq,
+        n_thread: n_thread, out_n: out_n, out_s: out_s, seed: seed,
+        xa_max: xa_max, mb_size: mb_size, max_mb_size: max_mb_size,
+        max_sw_mat: max_sw_mat, cap_kalloc: cap_kalloc
+      }
+    end
+
+    # Returns a compact representation of all option fields.
+    def inspect
+      "#<#{self.class.name} #{to_h.map { |k, v| "#{k}=#{v.inspect}" }.join(', ')}>"
+    end
+
+    private
+
+    # Called from C's initialize with a keyword-arguments Hash.
+    # @api private
+    def __keyword_new__(kwargs)
+      kwargs.each do |key, value|
+        setter = :"#{key}="
+        raise ArgumentError, "unknown option: #{key}" unless respond_to?(setter)
+
+        public_send(setter, value)
+      end
+    end
+  end
+end

data/lib/minibwa/sam.rb

@@ -0,0 +1,85 @@
+# frozen_string_literal: true
+
+module Minibwa
+  # SAM output built from Hit objects, in pure Ruby.
+  #
+  # Upstream's mb_fmt_sam() is deliberately not wrapped: it takes types that
+  # live in the private mbpriv.h (l2b_t, mb_bseq1_t) and would tie the gem to
+  # minibwa's internals. Doing it here also puts the soft clips that
+  # Hit#cigar omits back into the emitted CIGAR.
+  #
+  # == Reverse-strand alignments
+  #
+  # For reverse-strand alignments (Hit#rev == true), the SAM spec requires
+  # SEQ to be the reverse complement of the original query and the FLAG
+  # to have 0x10 set.  Sam.format does NOT do this automatically: callers
+  # must pass the already-oriented sequence and the correct flag.  This is
+  # because the library does not retain the original query sequence after
+  # mapping.
+  module Sam
+    module_function
+
+    # Generates a SAM header from an Index.
+    #
+    #   puts Minibwa::Sam.header(index)
+    def header(index, hd: nil, pg: nil, rg: nil)
+      lines = [hd || "@HD\tVN:1.6\tSO:unsorted"]
+
+      # Reference sequences from the index
+      tid = 0
+      while (name = index.ctg_name(tid))
+        len = index.ctg_len(tid)
+        lines << "@SQ\tSN:#{name}\tLN:#{len}"
+        tid += 1
+      end
+
+      lines << pg if pg
+      lines << rg if rg
+      lines.join("\n") + "\n"
+    end
+
+    # Formats a single alignment as a SAM line.
+    #
+    # +qname+::  query name.
+    # +flag+::   SAM flag (Integer).
+    # +hit+::    a Minibwa::Hit.
+    # +seq+::    the original query sequence.
+    # +qual+::   the original quality string (or "*").
+    # +mate+::   optional mate Hit for paired-end reads.
+    #
+    # Returns a SAM line String (without trailing newline).
+    def format(qname, flag, hit, seq, qual = '*', mate: nil)
+      rnext, pnext = if mate
+                       # '=' means the mate is on the same reference sequence.
+                       mate_ref = mate.ctg == hit.ctg && hit.ctg ? '=' : mate.ctg || '*'
+                       [mate_ref, mate.ts + 1]
+                     else
+                       ['*', 0]
+                     end
+
+      # For reverse-strand alignments the SEQ field should be the reverse
+      # complement of the original query (SAM spec).  Callers must pass the
+      # already-oriented sequence; see the module documentation at the top
+      # of this file.
+      # NM is the edit distance, not the number of suboptimal alignments.
+      # blen - mlen counts the non-matching positions within the alignment.
+      [
+        qname, flag, hit.ctg || '*', hit.ts + 1, hit.mapq,
+        build_full_cigar(hit, seq.length), rnext, pnext, 0,
+        seq || '*', qual || '*',
+        "NM:i:#{hit.blen - hit.mlen}", "AS:i:#{hit.score}"
+      ].join("\t")
+    end
+
+    # Builds the full CIGAR string including soft clips.
+    def build_full_cigar(hit, query_len)
+      parts = []
+      parts << "#{hit.qs}S" if hit.qs > 0
+      cigar = hit.cigar_str
+      parts << cigar unless cigar.empty?
+      soft_clip = query_len - hit.qe
+      parts << "#{soft_clip}S" if soft_clip > 0
+      parts.empty? ? '*' : parts.join
+    end
+  end
+end

data/lib/minibwa/version.rb

@@ -0,0 +1,6 @@
+# frozen_string_literal: true
+
+module Minibwa
+  # Gem version.
+  VERSION = '0.0.0'
+end

data/lib/minibwa.rb

@@ -0,0 +1,11 @@
+# frozen_string_literal: true
+
+require_relative 'minibwa/version'
+require 'minibwa/minibwa'
+
+require_relative 'minibwa/options'
+require_relative 'minibwa/index'
+require_relative 'minibwa/hit'
+require_relative 'minibwa/sam'
+
+# Minibwa::Error is defined in the C extension (minibwa.c).

metadata

@@ -0,0 +1,88 @@
+--- !ruby/object:Gem::Specification
+name: minibwa
+version: !ruby/object:Gem::Version
+  version: 0.0.0
+platform: ruby
+authors:
+- kojix2
+bindir: bin
+cert_chain: []
+date: 1980-01-02 00:00:00.000000000 Z
+dependencies: []
+executables: []
+extensions:
+- ext/minibwa/extconf.rb
+extra_rdoc_files: []
+files:
+- LICENSE.txt
+- README.md
+- ext/minibwa/extconf.rb
+- ext/minibwa/mb_buffer.c
+- ext/minibwa/mb_hit.c
+- ext/minibwa/mb_index.c
+- ext/minibwa/mb_index_build.c
+- ext/minibwa/mb_options.c
+- ext/minibwa/minibwa.c
+- ext/minibwa/minibwa.h
+- ext/minibwa/minibwa/LICENSE.txt
+- ext/minibwa/minibwa/align.c
+- ext/minibwa/minibwa/bseq.h
+- ext/minibwa/minibwa/bwt.c
+- ext/minibwa/minibwa/bwt.h
+- ext/minibwa/minibwa/cs.c
+- ext/minibwa/minibwa/format.c
+- ext/minibwa/minibwa/index.c
+- ext/minibwa/minibwa/kalloc.c
+- ext/minibwa/minibwa/kalloc.h
+- ext/minibwa/minibwa/ketopt.h
+- ext/minibwa/minibwa/kommon.c
+- ext/minibwa/minibwa/kommon.h
+- ext/minibwa/minibwa/kseq.h
+- ext/minibwa/minibwa/ksort.h
+- ext/minibwa/minibwa/ksw2.h
+- ext/minibwa/minibwa/ksw2_extd2_sse.c
+- ext/minibwa/minibwa/ksw2_extz2_sse.c
+- ext/minibwa/minibwa/ksw2_ll_sse.c
+- ext/minibwa/minibwa/kthread.h
+- ext/minibwa/minibwa/l2bit.c
+- ext/minibwa/minibwa/l2bit.h
+- ext/minibwa/minibwa/lchain.c
+- ext/minibwa/minibwa/libsais.c
+- ext/minibwa/minibwa/libsais.h
+- ext/minibwa/minibwa/libsais64.c
+- ext/minibwa/minibwa/libsais64.h
+- ext/minibwa/minibwa/map-algo.c
+- ext/minibwa/minibwa/mbpriv.h
+- ext/minibwa/minibwa/minibwa.h
+- ext/minibwa/minibwa/options.c
+- ext/minibwa/minibwa/pe.c
+- ext/minibwa/minibwa/s2n-lite.h
+- ext/minibwa/minibwa/seed.c
+- lib/minibwa.rb
+- lib/minibwa/hit.rb
+- lib/minibwa/index.rb
+- lib/minibwa/options.rb
+- lib/minibwa/sam.rb
+- lib/minibwa/version.rb
+homepage: https://github.com/kojix2/ruby-minibwa
+licenses:
+- MIT
+metadata: {}
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: 3.2.0
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubygems_version: 4.0.16
+specification_version: 4
+summary: Ruby bindings for minibwa, a short-read aligner
+test_files: []