bettersam 0.0.2 → 0.0.3

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Files changed (5) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +0 -2
  3. data/lib/bettersam.rb +6 -6
  4. data/test/test_test.rb +7 -2
  5. metadata +23 -22
checksums.yaml CHANGED
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+ metadata.gz: f6308aefe4a2681466d5fda521eaa167ecb2dea4dcefb9d7bf761f5c80b5ea771f01d0d65cc1a69922c063f01710e85f0c1cf2f9d7e2ed099b3367147f12f044
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data/README.md CHANGED
@@ -6,11 +6,9 @@ A SAM library for ruby, based on https://github.com/jesserod/samruby.
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  [![Gem Version](https://badge.fury.io/rb/bettersam.png)][gem]
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  [![Build Status](https://secure.travis-ci.org/Blahah/bettersam.png?branch=master)][travis]
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  [![Dependency Status](https://gemnasium.com/Blahah/bettersam.png?travis)][gemnasium]
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- [![Code Climate](https://codeclimate.com/github/Blahah/bettersam.png)][codeclimate]
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  [![Coverage Status](https://coveralls.io/repos/Blahah/bettersam/badge.png?branch=master)][coveralls]
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  [gem]: https://badge.fury.io/rb/bettersam
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  [travis]: https://travis-ci.org/Blahah/bettersam
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  [gemnasium]: https://gemnasium.com/Blahah/bettersam
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- [codeclimate]: https://codeclimate.com/github/Blahah/bettersam
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  [coveralls]: https://coveralls.io/r/Blahah/bettersam
data/lib/bettersam.rb CHANGED
@@ -5,7 +5,7 @@ class BetterSam
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  # value (i.e. value = 2^(i+1))
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  $flags = [
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  nil,
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- 0x1, # 1. read paired
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+ 0x1, # 1. read paired
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  0x2, # 2. read mapped in proper pair (i.e. with acceptable insert size)
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  0x4, # 3. read unmapped
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  0x8, # 4. mate unmapped
@@ -29,7 +29,7 @@ public
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  def parse_line(line)
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  return false if line[0] == "@"
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-
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+
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  f = line.chomp.split("\t", -1)
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  raise "SAM lines must have at least 11 fields (had #{f.size})" if f.size < 11
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@@ -52,7 +52,7 @@ public
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  while i < f.size
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  tag = f[i]
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  i += 1
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- colon_index = tag.rindex(':')
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+ colon_index = tag.rindex(':')
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  raise line if f.rindex == nil
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  key = tag[0, colon_index]
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  value = int_or_raw(tag[colon_index + 1, tag.size - colon_index] || "")
@@ -97,7 +97,7 @@ public
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  end
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  def primary_aln?
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- !(@flag & $flags[9]) != 0
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+ (@flag & $flags[9]) == 0
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  end
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  def quality_fail?
@@ -115,7 +115,7 @@ public
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  end
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  def pair_opposite_strands?
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- (!self.read_reverse_strand? && self.mate_reverse_strand?) ||
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+ (!self.read_reverse_strand? && self.mate_reverse_strand?) ||
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  (self.read_reverse_strand? && !self.mate_reverse_strand?)
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  end
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@@ -150,7 +150,7 @@ public
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  l = str.length
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  @cigar_list = []
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  while str.length>0
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- if str =~ /([0-9]+[MIDNSHPX=]+)/
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+ if str =~ /([0-9]+[MIDNSHPX=]+)/
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  @cigar_list << {$1[0..-2].to_i => $1[-1]}
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  str = str.slice($1.length, l)
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  else
data/test/test_test.rb CHANGED
@@ -13,6 +13,7 @@ class TestBetterSam < Test::Unit::TestCase
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  @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")
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  @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")
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  @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")
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+ @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 NM:i:0 MD:Z:71 YS:i:44 YT:Z:CP")
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  end
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  should "be a paired read" do
@@ -77,7 +78,7 @@ class TestBetterSam < Test::Unit::TestCase
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78
 
78
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  should "mark another snp" do
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  assert @l2.mark_snp(1789386)==2, "this is #{@l2.mark_snp(1789386)}, but i think it should be 3"
80
- end
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+ end
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  should "mark a third snp" do
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  assert @l3.mark_snp(1789386)==9, "this is #{@l3.mark_snp(1789386)}, but i think it should be 9"
@@ -89,5 +90,9 @@ class TestBetterSam < Test::Unit::TestCase
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  assert @l4r.put_snp==1789386, "this is #{@l4r.put_snp}, but I think it should be 1789386"
90
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  end
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+ should "not be primary alignment" do
94
+ assert !@l5l.primary_aln?
95
+ end
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+
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  end
93
- end
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+ end
metadata CHANGED
@@ -1,84 +1,84 @@
1
1
  --- !ruby/object:Gem::Specification
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  name: bettersam
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  version: !ruby/object:Gem::Version
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- version: 0.0.2
4
+ version: 0.0.3
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  platform: ruby
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  authors:
7
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  - Richard Smith
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- - Jesse Rodriguez
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+ - Chris Boursnell
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2014-05-07 00:00:00.000000000 Z
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+ date: 2014-06-30 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: simplecov
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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- - - ">="
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+ - - '>='
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  - !ruby/object:Gem::Version
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  version: '0'
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- type: :runtime
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+ type: :development
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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  requirements:
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- - - ">="
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+ - - '>='
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  - !ruby/object:Gem::Version
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  version: '0'
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  - !ruby/object:Gem::Dependency
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  name: rake
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
32
- - - ">="
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+ - - '>='
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  - !ruby/object:Gem::Version
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  version: '0'
35
- type: :runtime
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+ type: :development
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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  requirements:
39
- - - ">="
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+ - - '>='
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  - !ruby/object:Gem::Version
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  version: '0'
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  - !ruby/object:Gem::Dependency
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  name: turn
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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- - - ">="
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+ - - '>='
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  - !ruby/object:Gem::Version
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  version: '0'
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- type: :runtime
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+ type: :development
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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  requirements:
53
- - - ">="
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+ - - '>='
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  - !ruby/object:Gem::Version
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  version: '0'
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  - !ruby/object:Gem::Dependency
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  name: shoulda-context
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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- - - ">="
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+ - - '>='
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  - !ruby/object:Gem::Version
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  version: '0'
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- type: :runtime
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+ type: :development
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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  requirements:
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- - - ">="
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+ - - '>='
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  - !ruby/object:Gem::Version
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  version: '0'
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  - !ruby/object:Gem::Dependency
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  name: coveralls
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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- - - ">="
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+ - - '>='
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  - !ruby/object:Gem::Version
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  version: '0'
77
- type: :runtime
77
+ type: :development
78
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  prerelease: false
79
79
  version_requirements: !ruby/object:Gem::Requirement
80
80
  requirements:
81
- - - ">="
81
+ - - '>='
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82
  - !ruby/object:Gem::Version
83
83
  version: '0'
84
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  description: Extended SAM (Sequence Alignment/Map) file parsing
@@ -89,8 +89,8 @@ extra_rdoc_files: []
89
89
  files:
90
90
  - Rakefile
91
91
  - lib/bettersam.rb
92
- - test/test_test.rb
93
92
  - test/helper.rb
93
+ - test/test_test.rb
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  - README.md
95
95
  - LICENSE
96
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  homepage: https://github.com/blahah/bettersam
@@ -103,18 +103,19 @@ require_paths:
103
103
  - lib
104
104
  required_ruby_version: !ruby/object:Gem::Requirement
105
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  requirements:
106
- - - ">="
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+ - - '>='
107
107
  - !ruby/object:Gem::Version
108
108
  version: '0'
109
109
  required_rubygems_version: !ruby/object:Gem::Requirement
110
110
  requirements:
111
- - - ">="
111
+ - - '>='
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112
  - !ruby/object:Gem::Version
113
113
  version: '0'
114
114
  requirements: []
115
115
  rubyforge_project:
116
- rubygems_version: 2.1.4
116
+ rubygems_version: 2.0.6
117
117
  signing_key:
118
118
  specification_version: 4
119
119
  summary: Extended SAM file parsing
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120
  test_files: []
121
+ has_rdoc: