bettersam 0.1.1 → 0.2.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: adf55f7adc240db5cee1c5f188f3abd5798fbb98
-  data.tar.gz: 49f7b0e878392c32e49f18420777987fdcb252fc
+  metadata.gz: ebf104198d7b3ce4721ee95da8e6364049652351
+  data.tar.gz: 65fc1835e6563e44febdf76f9cc1feb7cd0c16b0
 SHA512:
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-  data.tar.gz: b73440febce482e72fecc812e0afde3478743e128a9bf43f1f6842cd1e28fff1b70786b8fae13a9f60c46803b7ab4ce29e3e844d5d2880e82cab8c23f4407dc3
+  metadata.gz: 0fc83632508d5254d030ff3e960db2a6c162fa6297fa0468888d32f377b4e60c003c3d08ef700eb1fda1cf92fa6fa51e5a05f8435ba154728c1e6f71f768e125
+  data.tar.gz: c6bfd6f772918cdfb08efaac2af693d23c8938924862f5aa68a87077183576a9d4c4c950c8a018f964b8f461bd0eb8248840f72ec49a69c6fb91fa594117c341

data/Rakefile

@@ -5,5 +5,15 @@ Rake::TestTask.new do |t|
 end
 
 desc "Run tests"
-task :default => :test
+task :default => ["ext:build", :test]
 
+namespace :ext do
+  desc "Build native extension"
+  task :build do
+    cd "ext"
+    ruby "mkrf_conf.rb"
+    sh "rake"
+    cd ".."
+  end
+
+end

data/lib/bettersam.rb

@@ -1,270 +1,34 @@
-class BetterSam
-
-  # meanings of SAM flag components, with index i
-  # being one more than the exponent 2 must be raised to to get the
-  # value (i.e. value = 2^(i+1))
-  $flags = [
-    nil,
-    0x1,  #    1. read paired
-    0x2,  #    2. read mapped in proper pair (i.e. with acceptable insert size)
-    0x4,  #    3. read unmapped
-    0x8,  #    4. mate unmapped
-    0x10,  #   5. read reverse strand
-    0x20,  #   6. mate reverse strand
-    0x40,  #   7. first in pair
-    0x80,  #   8. second in pair
-    0x100,  #  9. not primary alignment
-    0x200,  #  10. read fails platform/vendor quality checks
-    0x400]  #  11. read is PCR or optical duplicate
-
-public
-  attr_accessor :name, :flag, :chrom, :pos, :mapq, :cigar, :mchrom, :mpos
-  attr_accessor :insert, :seq, :qual, :tags, :length
-  attr_accessor :snp
-  attr_reader :cigar_list
-
-  def initialize(line=nil)
-    @tags = {}
-    parse_line(line) unless line.nil?
-  end
-
-  def parse_line(line)
-    return false if line[0] == "@"
-
-    f = line.chomp.split("\t", -1)
-    raise "SAM lines must have at least 11 fields (had #{f.size})" if f.size < 11
-
-    # colnames = %w(1:name 2:flag 3:chr 4:pos 5:mapq 6:cigar 7:mchr 8:mpos 9:insrt 10:seq 11:qual)
-
-    @name = f[0]
-    @flag = int_or_raw(f[1])
-    @chrom = f[2]
-    @pos = int_or_neg1(f[3])
-    @mapq = int_or_neg1(f[4])
-    @cigar = f[5]
-    @mchrom = f[6]
-    @mpos = int_or_neg1(f[7])
-    @insert = int_or_raw(f[8])
-    @seq = f[9]
-    @qual = f[10]
-    @length = nil
-
-    @tags = {}
-    i = 11
-    while i < f.size
-      tag = f[i]
-      i += 1
-      a = tag.split(":")
-      raise line if a.length != 3
-      if a[1]=="i"
-        @tags[a[0].to_sym] = a[2].to_i
-      elsif a[1]=="Z"
-        @tags[a[0].to_sym] = a[2]
-      else
-        @tags[a[0].to_sym] = a[2]
-      end
-    end
-
-    return true;
-  end
-
-  # flag parsing convenience methods
-
-  def read_paired?
-    @flag & $flags[1] != 0
-  end
-
-  def read_properly_paired?
-    @flag & $flags[2] != 0
-  end
-
-  def read_unmapped?
-    @flag & $flags[3] != 0
-  end
-
-  def mate_unmapped?
-    @flag & $flags[4] != 0
-  end
-
-  def read_reverse_strand?
-    @flag & $flags[5] != 0
-  end
-
-  def mate_reverse_strand?
-    @flag & $flags[6] != 0
-  end
-
-  def first_in_pair?
-    @flag & $flags[7] != 0
-  end
-
-  def second_in_pair?
-    @flag & $flags[8] !=0
-  end
-
-  def primary_aln?
-    (@flag & $flags[9]) == 0
-  end
-
-  def quality_fail?
-    @flag & $flags[10] != 0
-  end
+require 'ffi'
+require 'bettersam/library'
+require 'bettersam/samtagset'
+require 'bettersam/samrecord'
 
-  def pcr_duplicate?
-    @flag & $flags[11] != 0
-  end
-
-  # pair convenience methods
-
-  def both_mapped?
-    !(self.read_unmapped? && self.mate_unmapped?)
-  end
-
-  def pair_opposite_strands?
-    (!self.read_reverse_strand? && self.mate_reverse_strand?) ||
-      (self.read_reverse_strand? && !self.mate_reverse_strand?)
-  end
-
-  def pair_same_strand?
-    !self.pair_opposite_strands?
-  end
-
-  def edit_distance
-    @tags[:NM]
-  end
-
-  def length
-    @length = @seq.length if !@length
-    return @length
-  end
-
-  # cigar parsing methods
-
-  def exact_match?
-    @tags[:NM]==0
-  end
-
-  def endpos
-    if !@cigar_list
-      self.parse_cigar
-    end
-    e = @pos
-    @cigar_list.each do |h|
-      a = h.to_a
-      bases = a[0][0]
-      match = a[0][1]
-      if match =~ /[MD]/
-        e += bases
-      end
-    end
-    return e
-  end
-
-  def parse_cigar
-    str = @cigar
-    l = str.length
-    @cigar_list = []
-    while str.length>0
-      if str =~ /([0-9]+[MIDNSHPX=]+)/
-        @cigar_list << {$1[0..-2].to_i => $1[-1]}
-        str = str.slice($1.length, l)
-      else
-        puts str
-      end
-    end
-  end
+class BetterSam
 
-  # snp storing
+  extend FFI::Library
 
-  def contains_snp?(snp)
-    snp >= @pos and snp < self.endpos
-  end
+  ffi_lib Library.load
+  attach_function :sam_iterator, [SAMRecord], :int
+  attr_accessor :file
 
-  def mark_snp(snp)
-    if self.contains_snp?(snp)
-      if !@cigar_list
-        self.parse_cigar
-      end
-      p = @pos
-      s = snp
-      @cigar_list.each do |h|
-        if p > s and s >= @pos
-          @snp = s - @pos
-        else
-          a = h.to_a
-          bases = a[0][0]
-          match = a[0][1]
-          if match == "M"
-            p += bases
-          elsif match == "I"
-            s += bases
-          elsif match == "D"
-            s -= bases
-          end
-        end
-      end
-      if p > s and s >= @pos
-        @snp = s - @pos
-      end
-    end
-    @snp
+  def initialize file
+    self.file = file
   end
 
-  def transfer_snp(bs) # load in another bettersam object
-    if !self.read_unmapped? and !bs.read_unmapped?
-      if (self.read_reverse_strand? and bs.read_reverse_strand?) or (!self.read_reverse_strand? and !bs.read_reverse_strand?)
-        @snp = bs.snp
-      else
-      end
+  def each_record &block
+    if !File.exist?(self.file)
+      raise ArgumentError, "File #{self.file} does not exist"
     end
+    record = SAMRecord.new
+    record[:filename] = FFI::MemoryPointer.from_string(self.file)
+    result = nil
+    result = parse_sam(record, &block)
   end
 
-  def put_snp # find the location of a snp on the genome
-    if @snp
-      if !@cigar_list
-        self.parse_cigar
-      end
-      s = @snp
-      p = 0
-      @cigar_list.each do |h|
-        if p > s
-          return s+@pos
-        else
-          a = h.to_a
-          bases = a[0][0]
-          match = a[0][1]
-          if match=="M"
-            p += bases
-          elsif match=="D"
-            s += bases
-          elsif match=="I"
-            s -= bases
-          end
-        end
-      end
-      if p > s
-        return s+@pos
-      end
-    else
-      puts "need to run mark_snp and transfer_snp first"
-      return nil
+  def parse_sam(record, &block)
+    while (result = BetterSam::sam_iterator(record)) == 1
+      yield record
     end
-    return -1
   end
 
-  def get_base_at(p)
-    @seq[p]
-  end
-
-private
-
-  def int_or_neg1(x)
-    Integer(x) rescue -1
-  end
-
-  def int_or_raw(x)
-    Integer(x) rescue x
-  end
-
-
 end

data/lib/bettersam/library.rb

@@ -0,0 +1,25 @@
+class BetterSam
+  class Library
+
+    require 'rbconfig'
+
+    def self.lib_extension
+      case RbConfig::CONFIG['host_os']
+        when /linux/ then return 'so'
+        when /darwin/ then return 'dylib'
+        else raise NotImplementedError,
+          "Native library is not available for Windows platform"
+      end
+    end
+
+    # Load the correct library for the OS system in use
+    # @return [String] the absolute path for the filename of the shared library
+    # @note this method is called automatically when the module is loaded
+    def self.load
+      path = File.expand_path File.dirname(__FILE__)
+      path.gsub!(/lib\/bettersam/,'ext')
+      File.join(path,"libbettersam.#{self.lib_extension}")
+    end
+
+  end
+end

data/lib/bettersam/samrecord.rb

@@ -0,0 +1,225 @@
+class BetterSam
+
+  class SAMRecord < FFI::Struct
+
+    # meanings of SAM flag components, with index i
+    # being one more than the exponent 2 must be raised to to get the
+    # value (i.e. value = 2^(i+1))
+    $flags = [
+      nil,
+      0x1,    #  1. read paired
+      0x2,    #  2. read mapped in proper pair (i.e. with acceptable insert size)
+      0x4,    #  3. read unmapped
+      0x8,    #  4. mate unmapped
+      0x10,   #  5. read reverse strand
+      0x20,   #  6. mate reverse strand
+      0x40,   #  7. first in pair
+      0x80,   #  8. second in pair
+      0x100,  #  9. not primary alignment
+      0x200,  #  10. read fails platform/vendor quality checks
+      0x400   #  11. read is PCR or optical duplicate
+    ]
+
+    # NOTE: fields must be in the same order
+    # here as they are in the struct definition
+    # in bettersam.h
+    layout :qname,    :pointer,
+           :flag,     :int,
+           :rname,    :pointer,
+           :pos,      :int,
+           :mapq,     :int,
+           :cigar,    :pointer,
+           :rnext,    :pointer,
+           :pnext,    :int,
+           :tlen,     :int,
+           :seq,      :pointer,
+           :qual,     :pointer,
+           :tags,     :pointer,
+           :filename, :pointer,
+           :line,     :pointer,
+           :file,     :pointer
+
+    attr_accessor :insert, :length, :snp
+    attr_reader :cigar_list
+
+    def qname
+      self[:qname].read_string
+    end
+
+    def name
+      qname
+    end
+
+    def flag
+      self[:flag]
+    end
+
+    def rname
+      self[:rname].read_string
+    end
+
+    def chrome
+      rname
+    end
+
+    def pos
+      self[:pos]
+    end
+
+    def mapq
+      self[:mapq]
+    end
+
+    def cigar
+      self[:cigar].read_string
+    end
+
+    def rnext
+      self[:rnext].read_string
+    end
+
+    def mchrom
+      rnext
+    end
+
+    def pnext
+      self[:pnext]
+    end
+
+    def mpos
+      pnext
+    end
+
+    def tlen
+      self[:tlen]
+    end
+
+    def seq
+      self[:seq].read_string
+    end
+
+    def qual
+      self[:qual].read_string
+    end
+
+    # returns a SAMTagSet object
+    def tags
+      if !@tags
+        @tags = BetterSam::SAMTagSet.new(self[:tags])
+      end
+      @tags
+    end
+
+    # basic flag convenience methods
+
+    def read_paired?
+      flag & $flags[1] != 0
+    end
+
+    def read_properly_paired?
+      flag & $flags[2] != 0
+    end
+
+    def read_unmapped?
+      flag & $flags[3] != 0
+    end
+
+    def mate_unmapped?
+      flag & $flags[4] != 0
+    end
+
+    def read_reverse_strand?
+      flag & $flags[5] != 0
+    end
+
+    def mate_reverse_strand?
+      flag & $flags[6] != 0
+    end
+
+    def first_in_pair?
+      flag & $flags[7] != 0
+    end
+
+    def second_in_pair?
+      flag & $flags[8] !=0
+    end
+
+    def primary_aln?
+      (flag & $flags[9]) == 0
+    end
+
+    def quality_fail?
+      flag & $flags[10] != 0
+    end
+
+    def pcr_duplicate?
+      flag & $flags[11] != 0
+    end
+
+    # pair convenience methods
+
+    def both_mapped?
+      !(read_unmapped? && mate_unmapped?)
+    end
+
+    def pair_opposite_strands?
+      (!read_reverse_strand? && mate_reverse_strand?) ||
+        (read_reverse_strand? && !mate_reverse_strand?)
+    end
+
+    def pair_same_strand?
+      !pair_opposite_strands?
+    end
+
+    def edit_distance
+      tags.nm
+    end
+
+    def length
+      @length = seq.length if !@length
+      return @length
+    end
+
+    # cigar parsing methods
+
+    def exact_match?
+      tags.nm==0 && cigar=="#{seq.length}M"
+    end
+
+    def endpos
+      if !@cigar_list
+        parse_cigar
+      end
+      e = pos
+      @cigar_list.each do |h|
+        a = h.to_a
+        bases = a[0][0]
+        match = a[0][1]
+        if match =~ /[MD]/
+          e += bases
+        end
+      end
+      e
+    end
+
+    def parse_cigar
+      str = cigar
+      l = str.length
+      @cigar_list = []
+      while str.length>0
+        if str =~ /([0-9]+[MIDNSHPX=]+)/
+          @cigar_list << {$1[0..-2].to_i => $1[-1]}
+          str = str.slice($1.length, l)
+        else
+          puts str
+        end
+      end
+    end
+
+    def get_base_at p
+      seq[p]
+    end
+
+  end
+
+end

data/lib/bettersam/samtagset.rb

@@ -0,0 +1,23 @@
+class BetterSam
+
+  class SAMTagSet < FFI::Struct
+
+    # NOTE: fields must be in the same order
+    # here as they are in the struct definition
+    # in bettersam.h
+    layout :xm, :int,
+           :nm, :int
+
+    # returns the number of mismatches in the alignment
+    def xm
+      self[:xm]
+    end
+
+    # returns the edit distance between query and target
+    def nm
+      self[:nm]
+    end
+
+  end
+
+end

data/test/data/basic.sam

@@ -0,0 +1,6 @@
+FCC00CKABXX:2:1101:10117:6470#CAGATCAT	81	nivara_3s	1572276	40	100M	=	1571527	-849	AGGATCGGGCCTCGTGAGCCGACGGTGAGCGAGTTGTTGTTGTTCCATACGGGGGCGCCGGAGTTGGTGCTCCACAGCGGGCCGTTGAACGAGCTCGACG	ZbaX^_baX\_S]_ZdYccYebeffddZdbebdadc[bdVeeeceeeddggggggggggggggggegeggdffbfefegggggggggggggggggggggg	AS:i:-24	XN:i:0	XM:i:4	XO:i:0	XG:i:0	NM:i:0	MD:Z:1T1G3T0A91	YS:i:-5	YT:Z:DP
+FCC00CKABXX:2:1101:10117:6470#CAGATCAT	81	chromosome03	1789384	24	4M5I91M	=	1788782	-697	AGGATCGGGCCTCGTGAGCCGACGGTGAGCGAGTTGTTGTTGTTCCATACGGGGGCGCCGGAGTTGGTGCTCCACAGCGGGCCGTTGAACGAGCTCGACG	ZbaX^_baX\_S]_ZdYccYebeffddZdbebdadc[bdVeeeceeeddggggggggggggggggegeggdffbfefegggggggggggggggggggggg	AS:i:-38	XN:i:0	XM:i:3	XO:i:1	XG:i:5	NM:i:8	MD:Z:0C1T6G85	YS:i:-5	YT:Z:DP
+FCC00CKABXX:2:1101:19524:66398#CAGATCAT	145	chromosome03	1789377	23	4M1I2M1D93M	=	1788766	-711	GGAGGATCGGGCCTCGTGGGCCGACGGTGAGCGAGTTGTTGTTGTTCCATACGGGGGCGCCGGAGTTGGTGCTCCACAGCGGGCCGTTGAACGAGCTCGA	Bc`aaT\Y_]RLMKKMHEMV_T[Y[deaeeeaadbaaa\_feecedddddadfcegdcXdggcggggggggg`gfbecbcggggggggeggggggggggg	AS:i:-51	XN:i:0	XM:i:6	XO:i:2	XG:i:2	NM:i:8	MD:Z:2T0C2^A2T0A5G1A81	YS:i:0	YT:Z:DP
+FCC00CKABXX:2:1101:16909:83925#CAGATCAT	145	nivara_3s	1572267	23	5M2D3M2I3M1I86M	=	1571498	-868	GTCCTCCAGGAGGATCGGGCCTCGTGAGCCGACGGTGAGCGAGTTGTTGTTGTTCCATACGGGGGCGCCGGAGTTGGTGCTCCACAGCGGGCCGTTGAAC	BBBBBB_Z`cU]^SZS][]USKV[L`ac`dedeageeefagegagffdd`egedgggedgggggggdggggggggefeeeQgeagggggggggggggggg	AS:i:-53	XN:i:0	XM:i:4	XO:i:3	XG:i:5	NM:i:9	MD:Z:2G2^TG3T5T0A81	YS:i:0	YT:Z:DP
+FCC00CKABXX:2:1101:16909:83925#CAGATCAT	145	chromosome03	1789378	23	7M4I3M5I81M	=	1788753	-716	GTCCTCCAGGAGGATCGGGCCTCGTGAGCCGACGGTGAGCGAGTTGTTGTTGTTCCATACGGGGGCGCCGGAGTTGGTGCTCCACAGCGGGCCGTTGAAC	BBBBBB_Z`cU]^SZS][]USKV[L`ac`dedeageeefagegagffdd`egedgggedgggggggdggggggggefeeeQgeagggggggggggggggg	AS:i:-59	XN:i:0	XM:i:4	XO:i:2	XG:i:9	NM:i:13	MD:Z:3A1A2T6G75	YS:i:0	YT:Z:DP
+FCC2HFRACXX:7:2314:9299:67450#TGACCAAT	355	Sb02g000720.1	1186	18	71M	=	1238	-150	CGTCATCTTCTCTCATATATTTGTATCACCCATCCATCCATCTGCCTTCGATATGCATCTCCACTCCGCCG	__^cc]^\`eegea`ffdfghhfd]eghhfffef``degfhf_^gdfhfg_fghhhfdhffdfhffbeWcW	AS:i:142	XN:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:71	YS:i:44	YT:Z:CP

data/test/test_bettersam.rb

@@ -0,0 +1,122 @@
+#!/usr/bin/env	ruby
+
+require 'helper'
+
+class TestBetterSam < Test::Unit::TestCase
+
+  context "BetterSam" do
+
+    setup do
+      path = File.join(File.dirname(__FILE__), 'data', 'basic.sam')
+      @fs = BetterSam.new path
+      # this is run before each test
+      @l1 = BetterSam.new("FCC00CKABXX:2:1101:10117:6470#CAGATCAT	81	nivara_3s	1572276	40	100M	=	1571527	-849	AGGATCGGGCCTCGTGAGCCGACGGTGAGCGAGTTGTTGTTGTTCCATACGGGGGCGCCGGAGTTGGTGCTCCACAGCGGGCCGTTGAACGAGCTCGACG	ZbaX^_baX\_S]_ZdYccYebeffddZdbebdadc[bdVeeeceeeddggggggggggggggggegeggdffbfefegggggggggggggggggggggg	AS:i:-24	XN:i:0	XM:i:4	XO:i:0	XG:i:0	NM:i:0	MD:Z:1T1G3T0A91	YS:i:-5	YT:Z:DP")
+      @l2 = BetterSam.new("FCC00CKABXX:2:1101:10117:6470#CAGATCAT	81	chromosome03	1789384	24	4M5I91M	=	1788782	-697	AGGATCGGGCCTCGTGAGCCGACGGTGAGCGAGTTGTTGTTGTTCCATACGGGGGCGCCGGAGTTGGTGCTCCACAGCGGGCCGTTGAACGAGCTCGACG	ZbaX^_baX\_S]_ZdYccYebeffddZdbebdadc[bdVeeeceeeddggggggggggggggggegeggdffbfefegggggggggggggggggggggg	AS:i:-38	XN:i:0	XM:i:3	XO:i:1	XG:i:5	NM:i:8	MD:Z:0C1T6G85	YS:i:-5	YT:Z:DP")
+      @l3 = BetterSam.new("FCC00CKABXX:2:1101:19524:66398#CAGATCAT	145	chromosome03	1789377	23	4M1I2M1D93M	=	1788766	-711	GGAGGATCGGGCCTCGTGGGCCGACGGTGAGCGAGTTGTTGTTGTTCCATACGGGGGCGCCGGAGTTGGTGCTCCACAGCGGGCCGTTGAACGAGCTCGA	Bc`aaT\Y_]RLMKKMHEMV_T[Y[deaeeeaadbaaa\_feecedddddadfcegdcXdggcggggggggg`gfbecbcggggggggeggggggggggg	AS:i:-51	XN:i:0	XM:i:6	XO:i:2	XG:i:2	NM:i:8	MD:Z:2T0C2^A2T0A5G1A81	YS:i:0	YT:Z:DP")
+      @l4l = BetterSam.new("FCC00CKABXX:2:1101:16909:83925#CAGATCAT	145	nivara_3s	1572267	23	5M2D3M2I3M1I86M	=	1571498	-868	GTCCTCCAGGAGGATCGGGCCTCGTGAGCCGACGGTGAGCGAGTTGTTGTTGTTCCATACGGGGGCGCCGGAGTTGGTGCTCCACAGCGGGCCGTTGAAC	BBBBBB_Z`cU]^SZS][]USKV[L`ac`dedeageeefagegagffdd`egedgggedgggggggdggggggggefeeeQgeagggggggggggggggg	AS:i:-53	XN:i:0	XM:i:4	XO:i:3	XG:i:5	NM:i:9	MD:Z:2G2^TG3T5T0A81	YS:i:0	YT:Z:DP")
+      @l4r = BetterSam.new("FCC00CKABXX:2:1101:16909:83925#CAGATCAT	145	chromosome03	1789378	23	7M4I3M5I81M	=	1788753	-716	GTCCTCCAGGAGGATCGGGCCTCGTGAGCCGACGGTGAGCGAGTTGTTGTTGTTCCATACGGGGGCGCCGGAGTTGGTGCTCCACAGCGGGCCGTTGAAC	BBBBBB_Z`cU]^SZS][]USKV[L`ac`dedeageeefagegagffdd`egedgggedgggggggdggggggggefeeeQgeagggggggggggggggg	AS:i:-59	XN:i:0	XM:i:4	XO:i:2	XG:i:9	NM:i:13	MD:Z:3A1A2T6G75	YS:i:0	YT:Z:DP")
+      @l5l = BetterSam.new("FCC2HFRACXX:7:2314:9299:67450#TGACCAAT	355	Sb02g000720.1	1186	18	71M	=	1238	-150	CGTCATCTTCTCTCATATATTTGTATCACCCATCCATCCATCTGCCTTCGATATGCATCTCCACTCCGCCG	__^cc]^\`eegea`ffdfghhfd]eghhfffef``degfhf_^gdfhfg_fghhhfdhffdfhffbeWcW	AS:i:142	XN:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:71	YS:i:44	YT:Z:CP") #   NM:i:0
+    end
+
+    should "read a SAM file" do
+      expected = [
+        {:rname => "nivara_3s", :pos => 1572276, :xm => 4, :nm => 0},
+        {:rname => "chromosome03", :pos => 1789384, :xm => 3, :nm => 8},
+        {:rname => "chromosome03", :pos => 1789377, :xm => 6, :nm => 8},
+        {:rname => "nivara_3s", :pos => 1572267, :xm => 4, :nm => 9},
+        {:rname => "chromosome03", :pos => 1789378, :xm => 4, :nm => 13},
+        {:rname => "Sb02g000720.1", :pos => 1186, :xm => 0, :nm => 0}
+      ]
+      i = 0
+      @fs.each_record do |record|
+        assert_equal expected[i][:rname], record.rname, "chromosome"
+        assert_equal expected[i][:pos], record.pos, "position"
+        assert_equal expected[i][:xm], record.tags.xm, "mismatches"
+        assert_equal expected[i][:nm], record.tags.nm, "edit distance"
+        i += 1
+      end
+    end
+
+    should "detect a paired read" do
+      expected = [true, true, true, true, true, true]
+      i = 0
+      @fs.each_record do |record|
+        assert_equal expected[i], record.read_paired?, "record ##{i+1}"
+        i += 1
+      end
+    end
+
+    should "detect reverse strand" do
+      expected = [true, true, true, true, true, false]
+      i = 0
+      @fs.each_record do |record|
+        assert_equal expected[i], record.read_reverse_strand?, "record ##{i+1}"
+        i += 1
+      end
+    end
+
+    should "detect the first read in a pair" do
+      expected = [true, true, false, false, false, true]
+      i = 0
+      @fs.each_record do |record|
+        assert_equal expected[i], record.first_in_pair?, "record ##{i+1}"
+        i += 1
+      end
+    end
+
+    should "get the mapping position" do
+      expected = [1572276, 1789384, 1789377, 1572267, 1789378, 1186]
+      i = 0
+      @fs.each_record do |record|
+        assert_equal expected[i], record.pos, "record ##{i+1}"
+        i += 1
+      end
+    end
+
+    should "get the end position" do
+      expected = [1572276, 1789384, 1789377, 1572267, 1789378, 1186]
+      expected = expected.map { |x| x + 100 }
+      i = 0
+      @fs.each_record do |record|
+        assert_equal expected[i], record.endpos, "record ##{i+1}"
+        i += 1
+      end
+    end
+
+    should "detect exact matches" do
+      expected = [true, true, true, true, true, false]
+      i = 0
+      @fs.each_record do |record|
+        assert_equal expected[i], record.exact_match?, "record ##{i+1}"
+        i += 1
+      end
+    end
+
+    # should "give A" do
+    #   assert @l1.get_base_at(0)=="A", "this is #{@l1.get_base_at(0)}, but should be A"
+    # end
+    #
+    # should "parse cigar strings correctly" do
+    #   @l3.parse_cigar
+    #   assert @l3.cigar_list.size == 5
+    # end
+    #
+    # should "parse another cigar string correctly" do
+    #   @l4l.parse_cigar
+    #   assert @l4l.cigar_list.size == 7
+    # end
+    #
+    # should "not be primary alignment" do
+    #   assert !@l5l.primary_aln?
+    # end
+    #
+    # should "get the edit distance" do
+    #   assert_equal 8, @l2.tags[:NM]
+    # end
+    #
+    # should "fail to get the edit distance" do
+    #   assert_equal nil, @l5l.tags[:NM]
+    # end
+
+  end
+end

metadata

@@ -1,109 +1,122 @@
 --- !ruby/object:Gem::Specification
 name: bettersam
 version: !ruby/object:Gem::Version
-  version: 0.1.1
+  version: 0.2.0
 platform: ruby
 authors:
 - Richard Smith-Unna
 - Chris Boursnell
-- Jesse Rodriguez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-08-05 00:00:00.000000000 Z
+date: 2014-08-13 00:00:00.000000000 Z
 dependencies:
+- !ruby/object:Gem::Dependency
+  name: ffi
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: simplecov
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '0.8'
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.8.2
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '0.8'
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.8.2
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '10.3'
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 10.3.2
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '10.3'
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 10.3.2
 - !ruby/object:Gem::Dependency
   name: turn
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '0.9'
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.9.7
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '0.9'
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.9.7
 - !ruby/object:Gem::Dependency
   name: shoulda-context
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.2'
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.2.1
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.2'
-    - - '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.2.1
 - !ruby/object:Gem::Dependency
   name: coveralls
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '0.7'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '0.7'
 description: Extended SAM (Sequence Alignment/Map) file parsing
@@ -112,12 +125,16 @@ executables: []
 extensions: []
 extra_rdoc_files: []
 files:
+- LICENSE
+- README.md
 - Rakefile
 - lib/bettersam.rb
-- test/test_test.rb
+- lib/bettersam/library.rb
+- lib/bettersam/samrecord.rb
+- lib/bettersam/samtagset.rb
+- test/data/basic.sam
 - test/helper.rb
-- README.md
-- LICENSE
+- test/test_bettersam.rb
 homepage: https://github.com/blahah/bettersam
 licenses:
 - MIT
@@ -128,19 +145,18 @@ require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.1.4
+rubygems_version: 2.2.2
 signing_key: 
 specification_version: 4
 summary: Extended SAM file parsing
 test_files: []
-has_rdoc: 

data/test/test_test.rb

@@ -1,106 +0,0 @@
-#!/usr/bin/env	ruby
-
-require 'helper'
-
-class TestBetterSam < Test::Unit::TestCase
-
-  context "BetterSam" do
-
-    setup do
-      # this is run before each test
-      @l1 = BetterSam.new("FCC00CKABXX:2:1101:10117:6470#CAGATCAT	81	nivara_3s	1572276	40	100M	=	1571527	-849	AGGATCGGGCCTCGTGAGCCGACGGTGAGCGAGTTGTTGTTGTTCCATACGGGGGCGCCGGAGTTGGTGCTCCACAGCGGGCCGTTGAACGAGCTCGACG	ZbaX^_baX\_S]_ZdYccYebeffddZdbebdadc[bdVeeeceeeddggggggggggggggggegeggdffbfefegggggggggggggggggggggg	AS:i:-24	XN:i:0	XM:i:4	XO:i:0	XG:i:0	NM:i:0	MD:Z:1T1G3T0A91	YS:i:-5	YT:Z:DP")
-      @l2 = BetterSam.new("FCC00CKABXX:2:1101:10117:6470#CAGATCAT	81	chromosome03	1789384	24	4M5I91M	=	1788782	-697	AGGATCGGGCCTCGTGAGCCGACGGTGAGCGAGTTGTTGTTGTTCCATACGGGGGCGCCGGAGTTGGTGCTCCACAGCGGGCCGTTGAACGAGCTCGACG	ZbaX^_baX\_S]_ZdYccYebeffddZdbebdadc[bdVeeeceeeddggggggggggggggggegeggdffbfefegggggggggggggggggggggg	AS:i:-38	XN:i:0	XM:i:3	XO:i:1	XG:i:5	NM:i:8	MD:Z:0C1T6G85	YS:i:-5	YT:Z:DP")
-      @l3 = BetterSam.new("FCC00CKABXX:2:1101:19524:66398#CAGATCAT	145	chromosome03	1789377	23	4M1I2M1D93M	=	1788766	-711	GGAGGATCGGGCCTCGTGGGCCGACGGTGAGCGAGTTGTTGTTGTTCCATACGGGGGCGCCGGAGTTGGTGCTCCACAGCGGGCCGTTGAACGAGCTCGA	Bc`aaT\Y_]RLMKKMHEMV_T[Y[deaeeeaadbaaa\_feecedddddadfcegdcXdggcggggggggg`gfbecbcggggggggeggggggggggg	AS:i:-51	XN:i:0	XM:i:6	XO:i:2	XG:i:2	NM:i:8	MD:Z:2T0C2^A2T0A5G1A81	YS:i:0	YT:Z:DP")
-  	  @l4l = BetterSam.new("FCC00CKABXX:2:1101:16909:83925#CAGATCAT	145	nivara_3s	1572267	23	5M2D3M2I3M1I86M	=	1571498	-868	GTCCTCCAGGAGGATCGGGCCTCGTGAGCCGACGGTGAGCGAGTTGTTGTTGTTCCATACGGGGGCGCCGGAGTTGGTGCTCCACAGCGGGCCGTTGAAC	BBBBBB_Z`cU]^SZS][]USKV[L`ac`dedeageeefagegagffdd`egedgggedgggggggdggggggggefeeeQgeagggggggggggggggg	AS:i:-53	XN:i:0	XM:i:4	XO:i:3	XG:i:5	NM:i:9	MD:Z:2G2^TG3T5T0A81	YS:i:0	YT:Z:DP")
-	    @l4r = BetterSam.new("FCC00CKABXX:2:1101:16909:83925#CAGATCAT	145	chromosome03	1789378	23	7M4I3M5I81M	=	1788753	-716	GTCCTCCAGGAGGATCGGGCCTCGTGAGCCGACGGTGAGCGAGTTGTTGTTGTTCCATACGGGGGCGCCGGAGTTGGTGCTCCACAGCGGGCCGTTGAAC	BBBBBB_Z`cU]^SZS][]USKV[L`ac`dedeageeefagegagffdd`egedgggedgggggggdggggggggefeeeQgeagggggggggggggggg	AS:i:-59	XN:i:0	XM:i:4	XO:i:2	XG:i:9	NM:i:13	MD:Z:3A1A2T6G75	YS:i:0	YT:Z:DP")
-      @l5l = BetterSam.new("FCC2HFRACXX:7:2314:9299:67450#TGACCAAT	355	Sb02g000720.1	1186	18	71M	=	1238	-150	CGTCATCTTCTCTCATATATTTGTATCACCCATCCATCCATCTGCCTTCGATATGCATCTCCACTCCGCCG	__^cc]^\`eegea`ffdfghhfd]eghhfffef``degfhf_^gdfhfg_fghhhfdhffdfhffbeWcW	AS:i:142	XN:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:71	YS:i:44	YT:Z:CP") #   NM:i:0
-    end
-
-    should "be a paired read" do
-      assert @l1.read_paired?
-    end
-
-    should "be on the reverse strand" do
-      assert @l1.read_reverse_strand?
-    end
-
-    should "be the first pair" do
-      assert @l1.first_in_pair?
-    end
-
-    should "get the mappping position" do
-      assert @l1.pos == 1572276
-    end
-
-    should "get the end position" do
-      assert @l1.endpos == 1572376
-    end
-
-    should "get the end position too" do
-      assert @l2.endpos == 1789479, "this is #{@l1.endpos} but should be 1789479"
-    end
-
-    should "be exact match" do
-      assert @l1.exact_match?
-    end
-
-    should "contain snp" do
-      assert @l1.contains_snp?(1572283)
-    end
-
-    should "give A" do
-      assert @l1.get_base_at(0)=="A", "this is #{@l1.get_base_at(0)}, but should be A"
-    end
-
-    should "parse the cigar string correctly" do
-      @l3.parse_cigar
-      assert @l3.cigar_list.size == 5
-    end
-
-    should "parse another cigar string correctly" do
-      @l4l.parse_cigar
-      assert @l4l.cigar_list.size == 7
-    end
-
-    should "mark a snp" do
-      assert @l1.mark_snp(1572283)==7, "this is #{@l1.mark_snp(1572283)}, but i think it should be 7"
-    end
-
-    should "mark yet another snp" do
-      assert @l4l.mark_snp(1572283)==17, "this is #{@l4l.mark_snp(1572283)}, but i think it should be 17"
-    end
-
-    should "transfer a snp from one object to another" do
-      @l1.mark_snp(1572283)
-      @l2.transfer_snp(@l1)
-      assert @l2.snp == 7, "this is #{@l2.snp}, but i think it should be 7"
-    end
-
-    should "mark another snp" do
-      assert @l2.mark_snp(1789386)==2, "this is #{@l2.mark_snp(1789386)}, but i think it should be 3"
-    end
-
-    should "mark a third snp" do
-      assert @l3.mark_snp(1789386)==9, "this is #{@l3.mark_snp(1789386)}, but i think it should be 9"
-    end
-
-    should "find the location of a snp on the genome" do
-      @l4l.mark_snp(1572283)
-      @l4r.transfer_snp(@l4l)
-      assert @l4r.put_snp==1789386, "this is #{@l4r.put_snp}, but I think it should be 1789386"
-    end
-
-    should "not be primary alignment" do
-      assert !@l5l.primary_aln?
-    end
-
-    should "get the edit distance" do
-      assert_equal 8, @l2.tags[:NM]
-    end
-
-    should "fail to get the edit distance" do
-      assert_equal nil, @l5l.tags[:NM]
-    end
-
-  end
-end