bettersam 0.0.2 → 0.0.3

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.
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
@@ -1,7 +1,7 @@
1
1
  ---
2
2
  SHA1:
3
- metadata.gz: 7c1a3a8ba1fafb9fce91bc76a62d3869a4c60b5e
4
- data.tar.gz: 477b54306d56e399ce7a996dcd8f80ef5db44fd6
3
+ metadata.gz: a61794c089e1bbc0b2c7b5aebdf080cb0018a508
4
+ data.tar.gz: bf147789ee59d30182c24d6535618b919a8d3938
5
5
  SHA512:
6
- metadata.gz: 6d8d6e1e3d2ff18fb3021a0eb4357da7de7b8d1669ed2d0313dff291bf7093d58ab006fa65d54f933af898f2cb4dc7109621a031ab5118a778902b53bd15e2c1
7
- data.tar.gz: 5145d5824bbc7891e900cdddb9b80fe1de837fb28c5467a5ec2d3eb55a5402c3ff1588d56703626cef133519310993f0c8d8181f72ab217a60800f2dfb55f1ab
6
+ metadata.gz: f6308aefe4a2681466d5fda521eaa167ecb2dea4dcefb9d7bf761f5c80b5ea771f01d0d65cc1a69922c063f01710e85f0c1cf2f9d7e2ed099b3367147f12f044
7
+ data.tar.gz: 9938db788b714bea439ef342695676fcf90c2febcae8284e8dc3a4adf04979179d1904e331ce481aa428ba54cca083d8024535e8de07c6bf8cb57c40a7baa87d
data/README.md CHANGED
@@ -6,11 +6,9 @@ A SAM library for ruby, based on https://github.com/jesserod/samruby.
6
6
  [![Gem Version](https://badge.fury.io/rb/bettersam.png)][gem]
7
7
  [![Build Status](https://secure.travis-ci.org/Blahah/bettersam.png?branch=master)][travis]
8
8
  [![Dependency Status](https://gemnasium.com/Blahah/bettersam.png?travis)][gemnasium]
9
- [![Code Climate](https://codeclimate.com/github/Blahah/bettersam.png)][codeclimate]
10
9
  [![Coverage Status](https://coveralls.io/repos/Blahah/bettersam/badge.png?branch=master)][coveralls]
11
10
 
12
11
  [gem]: https://badge.fury.io/rb/bettersam
13
12
  [travis]: https://travis-ci.org/Blahah/bettersam
14
13
  [gemnasium]: https://gemnasium.com/Blahah/bettersam
15
- [codeclimate]: https://codeclimate.com/github/Blahah/bettersam
16
14
  [coveralls]: https://coveralls.io/r/Blahah/bettersam
data/lib/bettersam.rb CHANGED
@@ -5,7 +5,7 @@ class BetterSam
5
5
  # value (i.e. value = 2^(i+1))
6
6
  $flags = [
7
7
  nil,
8
- 0x1, # 1. read paired
8
+ 0x1, # 1. read paired
9
9
  0x2, # 2. read mapped in proper pair (i.e. with acceptable insert size)
10
10
  0x4, # 3. read unmapped
11
11
  0x8, # 4. mate unmapped
@@ -29,7 +29,7 @@ public
29
29
 
30
30
  def parse_line(line)
31
31
  return false if line[0] == "@"
32
-
32
+
33
33
  f = line.chomp.split("\t", -1)
34
34
  raise "SAM lines must have at least 11 fields (had #{f.size})" if f.size < 11
35
35
 
@@ -52,7 +52,7 @@ public
52
52
  while i < f.size
53
53
  tag = f[i]
54
54
  i += 1
55
- colon_index = tag.rindex(':')
55
+ colon_index = tag.rindex(':')
56
56
  raise line if f.rindex == nil
57
57
  key = tag[0, colon_index]
58
58
  value = int_or_raw(tag[colon_index + 1, tag.size - colon_index] || "")
@@ -97,7 +97,7 @@ public
97
97
  end
98
98
 
99
99
  def primary_aln?
100
- !(@flag & $flags[9]) != 0
100
+ (@flag & $flags[9]) == 0
101
101
  end
102
102
 
103
103
  def quality_fail?
@@ -115,7 +115,7 @@ public
115
115
  end
116
116
 
117
117
  def pair_opposite_strands?
118
- (!self.read_reverse_strand? && self.mate_reverse_strand?) ||
118
+ (!self.read_reverse_strand? && self.mate_reverse_strand?) ||
119
119
  (self.read_reverse_strand? && !self.mate_reverse_strand?)
120
120
  end
121
121
 
@@ -150,7 +150,7 @@ public
150
150
  l = str.length
151
151
  @cigar_list = []
152
152
  while str.length>0
153
- if str =~ /([0-9]+[MIDNSHPX=]+)/
153
+ if str =~ /([0-9]+[MIDNSHPX=]+)/
154
154
  @cigar_list << {$1[0..-2].to_i => $1[-1]}
155
155
  str = str.slice($1.length, l)
156
156
  else
data/test/test_test.rb CHANGED
@@ -13,6 +13,7 @@ class TestBetterSam < Test::Unit::TestCase
13
13
  @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")
14
14
  @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")
15
15
  @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")
16
+ @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")
16
17
  end
17
18
 
18
19
  should "be a paired read" do
@@ -77,7 +78,7 @@ class TestBetterSam < Test::Unit::TestCase
77
78
 
78
79
  should "mark another snp" do
79
80
  assert @l2.mark_snp(1789386)==2, "this is #{@l2.mark_snp(1789386)}, but i think it should be 3"
80
- end
81
+ end
81
82
 
82
83
  should "mark a third snp" do
83
84
  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
89
90
  assert @l4r.put_snp==1789386, "this is #{@l4r.put_snp}, but I think it should be 1789386"
90
91
  end
91
92
 
93
+ should "not be primary alignment" do
94
+ assert !@l5l.primary_aln?
95
+ end
96
+
92
97
  end
93
- end
98
+ end
metadata CHANGED
@@ -1,84 +1,84 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: bettersam
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.0.2
4
+ version: 0.0.3
5
5
  platform: ruby
6
6
  authors:
7
7
  - Richard Smith
8
- - Jesse Rodriguez
8
+ - Chris Boursnell
9
9
  autorequire:
10
10
  bindir: bin
11
11
  cert_chain: []
12
- date: 2014-05-07 00:00:00.000000000 Z
12
+ date: 2014-06-30 00:00:00.000000000 Z
13
13
  dependencies:
14
14
  - !ruby/object:Gem::Dependency
15
15
  name: simplecov
16
16
  requirement: !ruby/object:Gem::Requirement
17
17
  requirements:
18
- - - ">="
18
+ - - '>='
19
19
  - !ruby/object:Gem::Version
20
20
  version: '0'
21
- type: :runtime
21
+ type: :development
22
22
  prerelease: false
23
23
  version_requirements: !ruby/object:Gem::Requirement
24
24
  requirements:
25
- - - ">="
25
+ - - '>='
26
26
  - !ruby/object:Gem::Version
27
27
  version: '0'
28
28
  - !ruby/object:Gem::Dependency
29
29
  name: rake
30
30
  requirement: !ruby/object:Gem::Requirement
31
31
  requirements:
32
- - - ">="
32
+ - - '>='
33
33
  - !ruby/object:Gem::Version
34
34
  version: '0'
35
- type: :runtime
35
+ type: :development
36
36
  prerelease: false
37
37
  version_requirements: !ruby/object:Gem::Requirement
38
38
  requirements:
39
- - - ">="
39
+ - - '>='
40
40
  - !ruby/object:Gem::Version
41
41
  version: '0'
42
42
  - !ruby/object:Gem::Dependency
43
43
  name: turn
44
44
  requirement: !ruby/object:Gem::Requirement
45
45
  requirements:
46
- - - ">="
46
+ - - '>='
47
47
  - !ruby/object:Gem::Version
48
48
  version: '0'
49
- type: :runtime
49
+ type: :development
50
50
  prerelease: false
51
51
  version_requirements: !ruby/object:Gem::Requirement
52
52
  requirements:
53
- - - ">="
53
+ - - '>='
54
54
  - !ruby/object:Gem::Version
55
55
  version: '0'
56
56
  - !ruby/object:Gem::Dependency
57
57
  name: shoulda-context
58
58
  requirement: !ruby/object:Gem::Requirement
59
59
  requirements:
60
- - - ">="
60
+ - - '>='
61
61
  - !ruby/object:Gem::Version
62
62
  version: '0'
63
- type: :runtime
63
+ type: :development
64
64
  prerelease: false
65
65
  version_requirements: !ruby/object:Gem::Requirement
66
66
  requirements:
67
- - - ">="
67
+ - - '>='
68
68
  - !ruby/object:Gem::Version
69
69
  version: '0'
70
70
  - !ruby/object:Gem::Dependency
71
71
  name: coveralls
72
72
  requirement: !ruby/object:Gem::Requirement
73
73
  requirements:
74
- - - ">="
74
+ - - '>='
75
75
  - !ruby/object:Gem::Version
76
76
  version: '0'
77
- type: :runtime
77
+ type: :development
78
78
  prerelease: false
79
79
  version_requirements: !ruby/object:Gem::Requirement
80
80
  requirements:
81
- - - ">="
81
+ - - '>='
82
82
  - !ruby/object:Gem::Version
83
83
  version: '0'
84
84
  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
94
94
  - README.md
95
95
  - LICENSE
96
96
  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
105
  requirements:
106
- - - ">="
106
+ - - '>='
107
107
  - !ruby/object:Gem::Version
108
108
  version: '0'
109
109
  required_rubygems_version: !ruby/object:Gem::Requirement
110
110
  requirements:
111
- - - ">="
111
+ - - '>='
112
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
120
120
  test_files: []
121
+ has_rdoc: