bio-faster 0.2.2 → 0.4.2
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.
- data/.travis.yml +2 -3
- data/Gemfile +2 -0
- data/Gemfile.lock +2 -0
- data/LICENSE.txt +1 -1
- data/README.md +2 -3
- data/Rakefile +9 -15
- data/VERSION +1 -1
- data/bio-faster.gemspec +56 -12
- data/ext/faster.c +115 -52
- data/ext/mkrf_conf.rb +40 -0
- data/lib/bio-faster.rb +5 -4
- data/lib/bio/faster.rb +57 -0
- data/lib/bio/faster/library.rb +26 -0
- data/spec/fastq_error_spec.rb +55 -0
- data/spec/parser_spec.rb +28 -116
- data/test/data/errors/error_header.fastq +20 -0
- data/test/data/errors/error_long_qual.fastq +20 -0
- data/test/data/errors/error_qual_del.fastq +20 -0
- data/test/data/errors/error_qual_escape.fastq +20 -0
- data/test/data/errors/error_qual_null.fastq +0 -0
- data/test/data/errors/error_qual_space.fastq +20 -0
- data/test/data/errors/error_qual_tab.fastq +20 -0
- data/test/data/errors/error_qual_unit_sep.fastq +20 -0
- data/test/data/errors/error_qual_vtab.fastq +20 -0
- data/test/data/errors/error_spaces.fastq +20 -0
- data/test/data/errors/error_tabs.fastq +21 -0
- data/test/data/errors/error_trunc_at_qual.fastq +19 -0
- data/test/data/errors/error_trunc_at_seq.fastq +18 -0
- data/test/data/errors/error_trunc_in_qual.fastq +20 -0
- data/test/data/errors/error_trunc_in_seq.fastq +18 -0
- data/test/data/formats/illumina_full_range_as_illumina.fastq +8 -0
- data/test/data/formats/illumina_full_range_as_sanger.fastq +8 -0
- data/test/data/formats/illumina_full_range_as_solexa.fastq +8 -0
- data/test/data/formats/illumina_full_range_original_illumina.fastq +8 -0
- data/test/data/formats/longreads_as_illumina.fastq +40 -0
- data/test/data/formats/longreads_as_sanger.fastq +40 -0
- data/test/data/formats/longreads_as_solexa.fastq +40 -0
- data/test/data/formats/misc_dna_as_illumina.fastq +16 -0
- data/test/data/formats/misc_dna_as_sanger.fastq +16 -0
- data/test/data/formats/misc_dna_as_solexa.fastq +16 -0
- data/test/data/formats/misc_dna_original_sanger.fastq +16 -0
- data/test/data/formats/misc_rna_as_illumina.fastq +16 -0
- data/test/data/formats/misc_rna_as_sanger.fastq +16 -0
- data/test/data/formats/misc_rna_as_solexa.fastq +16 -0
- data/test/data/formats/misc_rna_original_sanger.fastq +16 -0
- data/test/data/formats/sanger_full_range_as_illumina.fastq +8 -0
- data/test/data/formats/sanger_full_range_as_sanger.fastq +8 -0
- data/test/data/formats/sanger_full_range_as_solexa.fastq +8 -0
- data/test/data/formats/sanger_full_range_original_sanger.fastq +8 -0
- data/test/data/formats/solexa_full_range_as_illumina.fastq +8 -0
- data/test/data/formats/solexa_full_range_as_sanger.fastq +8 -0
- data/test/data/formats/solexa_full_range_as_solexa.fastq +8 -0
- data/test/data/formats/solexa_full_range_original_solexa.fastq +8 -0
- data/test/data/formats/wrapping_as_illumina.fastq +12 -0
- data/test/data/formats/wrapping_as_sanger.fastq +12 -0
- data/test/data/formats/wrapping_as_solexa.fastq +12 -0
- metadata +88 -24
- data/ext/extconf.rb +0 -7
- data/ext/kseq.h +0 -223
- data/test/data/sample.fasta +0 -10
- data/test/data/sample.fastq +0 -24
- data/test/data/sample.fastq.gz +0 -0
- data/test/data/sff_sample.fastq +0 -16
|
@@ -0,0 +1,16 @@
|
|
|
1
|
+
@FAKE0011 Original version has lower case unambiguous RNA with PHRED scores from 0 to 40 inclusive (in that order)
|
|
2
|
+
ACGUACGUACGUACGUACGUACGUACGUACGUACGUACGUA
|
|
3
|
+
+
|
|
4
|
+
!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI
|
|
5
|
+
@FAKE0012 Original version has mixed case unambiguous RNA with PHRED scores from 0 to 40 inclusive (in that order)
|
|
6
|
+
gUcauAGcgUcauAGcgUcauAGcgUcauAGcgUcauAGcg
|
|
7
|
+
+
|
|
8
|
+
!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI
|
|
9
|
+
@FAKE0013 Original version has lower case unambiguous RNA with PHRED scores from 0 to 40 inclusive (in that order)
|
|
10
|
+
ucagucagucagucagucagucagucagucagucagucagu
|
|
11
|
+
+
|
|
12
|
+
!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI
|
|
13
|
+
@FAKE0014 Original version has mixed case ambiguous RNA with PHRED scores from 35 to 40 inclusive (cycled)
|
|
14
|
+
gaucrywsmkhbvdnGAUCRYWSMKHBVDN
|
|
15
|
+
+
|
|
16
|
+
DEFGHIDEFGHIDEFGHIDEFGHIDEFGHI
|
|
@@ -0,0 +1,8 @@
|
|
|
1
|
+
@FAKE0001 Original version has PHRED scores from 0 to 93 inclusive (in that order)
|
|
2
|
+
ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC
|
|
3
|
+
+
|
|
4
|
+
@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
5
|
+
@FAKE0002 Original version has PHRED scores from 93 to 0 inclusive (in that order)
|
|
6
|
+
CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA
|
|
7
|
+
+
|
|
8
|
+
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@
|
|
@@ -0,0 +1,8 @@
|
|
|
1
|
+
@FAKE0001 Original version has PHRED scores from 0 to 93 inclusive (in that order)
|
|
2
|
+
ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC
|
|
3
|
+
+
|
|
4
|
+
!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
|
|
5
|
+
@FAKE0002 Original version has PHRED scores from 93 to 0 inclusive (in that order)
|
|
6
|
+
CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA
|
|
7
|
+
+
|
|
8
|
+
~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,+*)('&%$#"!
|
|
@@ -0,0 +1,8 @@
|
|
|
1
|
+
@FAKE0001 Original version has PHRED scores from 0 to 93 inclusive (in that order)
|
|
2
|
+
ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC
|
|
3
|
+
+
|
|
4
|
+
;;>@BCEFGHJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
5
|
+
@FAKE0002 Original version has PHRED scores from 93 to 0 inclusive (in that order)
|
|
6
|
+
CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA
|
|
7
|
+
+
|
|
8
|
+
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJHGFECB@>;;
|
|
@@ -0,0 +1,8 @@
|
|
|
1
|
+
@FAKE0001 Original version has PHRED scores from 0 to 93 inclusive (in that order)
|
|
2
|
+
ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC
|
|
3
|
+
+
|
|
4
|
+
!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
|
|
5
|
+
@FAKE0002 Original version has PHRED scores from 93 to 0 inclusive (in that order)
|
|
6
|
+
CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA
|
|
7
|
+
+
|
|
8
|
+
~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,+*)('&%$#"!
|
|
@@ -0,0 +1,8 @@
|
|
|
1
|
+
@FAKE0003 Original version has Solexa scores from -5 to 62 inclusive (in that order)
|
|
2
|
+
ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
|
|
3
|
+
+
|
|
4
|
+
AABBCCDDEEFGHIJJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
|
|
5
|
+
@FAKE0004 Original version has Solexa scores from 62 to -5 inclusive (in that order)
|
|
6
|
+
TGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA
|
|
7
|
+
+
|
|
8
|
+
~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJJIHGFEEDDCCBBAA
|
|
@@ -0,0 +1,8 @@
|
|
|
1
|
+
@FAKE0003 Original version has Solexa scores from -5 to 62 inclusive (in that order)
|
|
2
|
+
ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
|
|
3
|
+
+
|
|
4
|
+
""##$$%%&&'()*++,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_
|
|
5
|
+
@FAKE0004 Original version has Solexa scores from 62 to -5 inclusive (in that order)
|
|
6
|
+
TGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA
|
|
7
|
+
+
|
|
8
|
+
_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,++*)('&&%%$$##""
|
|
@@ -0,0 +1,8 @@
|
|
|
1
|
+
@FAKE0003 Original version has Solexa scores from -5 to 62 inclusive (in that order)
|
|
2
|
+
ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
|
|
3
|
+
+
|
|
4
|
+
;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
|
|
5
|
+
@FAKE0004 Original version has Solexa scores from 62 to -5 inclusive (in that order)
|
|
6
|
+
TGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA
|
|
7
|
+
+
|
|
8
|
+
~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;
|
|
@@ -0,0 +1,8 @@
|
|
|
1
|
+
@FAKE0003 Original version has Solexa scores from -5 to 62 inclusive (in that order)
|
|
2
|
+
ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
|
|
3
|
+
+
|
|
4
|
+
;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
|
|
5
|
+
@FAKE0004 Original version has Solexa scores from 62 to -5 inclusive (in that order)
|
|
6
|
+
TGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA
|
|
7
|
+
+
|
|
8
|
+
~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;
|
|
@@ -0,0 +1,12 @@
|
|
|
1
|
+
@SRR014849.50939 EIXKN4201BA2EC length=135
|
|
2
|
+
GAAATTTCAGGGCCACCTTTTTTTTGATAGAATAATGGAGAAAATTAAAAGCTGTACATATACCAATGAACAATAAATCAATACATAAAAAAGGAGAAGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGG
|
|
3
|
+
+
|
|
4
|
+
Zb^Ld`N\[d`NaZ[aZc]UOKHDA[\YT[_W[aZ\aZ[Zd`SF_WeaUI[Y\[[\\\[\Z\aY`X[[aZ\aZ\d`OY[aY[[\[[e`WPJC^UZ[`X\[R]T_V_W[`[Ga\I`\H[[Q^TVa\Ia\Ic^LY\S
|
|
5
|
+
@SRR014849.110027 EIXKN4201APUB0 length=131
|
|
6
|
+
CTTCAAATGATTCCGGGACTGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTTCGGTTCCAACTCGCCGTCCGAATAATCCGTTCAAAATCTTGGCCTGTCAAAACGACTTTACGACCAGAACGATCCG
|
|
7
|
+
+
|
|
8
|
+
\aYY_[FY\T`X^Vd`OY\[[^U_V[R^T[_ZDc^La\HYYO\S[c^Ld`Nc_QAZaZaYaY`XZZ\[aZZ[aZ[aZ[aZY`Z[`ZWeaVJ\[aZaY`X[PY\eaUG[\[[d`OXTUZ[Q\\`W\\\Y_W\
|
|
9
|
+
@SRR014849.203935 EIXKN4201B4HU6 length=144
|
|
10
|
+
AACCCGTCCCATCAAAGATTTTGGTTGGAACCCGAAAGGGTTTTGAATTCAAACCCCTTTCGGTTCCAACTATTCAATTGTTTAACTTTTTTTAAATTGATGGTCTGTTGGACCATTTGTAATAATCCCCATCGGAATTTCTTT
|
|
11
|
+
+
|
|
12
|
+
`Z_ZDVT^YB[[Xd`PZ\d`RDaZaZ`ZaZ_ZDXd`Pd`Pd`RD[aZ`ZWd`Oc_RCd`P\aZ`ZaZaZY\YaZYaY`XYd`O`X[e`WPJEAc^LaZS[YYN[Z\Y`XWLT^U\b]JW[[RZ\SYc`RD[Z\WLXM`\HYa\I
|
|
@@ -0,0 +1,12 @@
|
|
|
1
|
+
@SRR014849.50939 EIXKN4201BA2EC length=135
|
|
2
|
+
GAAATTTCAGGGCCACCTTTTTTTTGATAGAATAATGGAGAAAATTAAAAGCTGTACATATACCAATGAACAATAAATCAATACATAAAAAAGGAGAAGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGG
|
|
3
|
+
+
|
|
4
|
+
;C?-EA/=<EA/B;<B;D>60,)%"<=:5<@8<B;=B;<;EA4'@8FB6*<:=<<===<=;=B:A9<<B;=B;=EA0:<B:<<=<<FA81+$?6;<A9=<3>5@7@8<A<(B=*A=)<<2?57B=*B=*D?-:=4
|
|
5
|
+
@SRR014849.110027 EIXKN4201APUB0 length=131
|
|
6
|
+
CTTCAAATGATTCCGGGACTGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTTCGGTTCCAACTCGCCGTCCGAATAATCCGTTCAAAATCTTGGCCTGTCAAAACGACTTTACGACCAGAACGATCCG
|
|
7
|
+
+
|
|
8
|
+
=B::@<':=5A9?7EA0:=<<?6@7<3?5<@;%D?-B=)::0=4<D?-EA/D@2";B;B:B:A9;;=<B;;<B;<B;<B;:A;<A;8FB7+=<B;B:A9<1:=FB6(<=<<EA0956;<2==A8===:@8=
|
|
9
|
+
@SRR014849.203935 EIXKN4201B4HU6 length=144
|
|
10
|
+
AACCCGTCCCATCAAAGATTTTGGTTGGAACCCGAAAGGGTTTTGAATTCAAACCCCTTTCGGTTCCAACTATTCAATTGTTTAACTTTTTTTAAATTGATGGTCTGTTGGACCATTTGTAATAATCCCCATCGGAATTTCTTT
|
|
11
|
+
+
|
|
12
|
+
A;@;%75?:#<<9EA1;=EA3%B;B;A;B;@;%9EA1EA1EA3%<B;A;8EA0D@3$EA1=B;A;B;B;:=:B;:B:A9:EA0A9<FA81+&"D?-B;4<::/<;=:A98-5?6=C>+8<<3;=4:DA3%<;=8-9.A=):B=*
|
|
@@ -0,0 +1,12 @@
|
|
|
1
|
+
@SRR014849.50939 EIXKN4201BA2EC length=135
|
|
2
|
+
GAAATTTCAGGGCCACCTTTTTTTTGATAGAATAATGGAGAAAATTAAAAGCTGTACATATACCAATGAACAATAAATCAATACATAAAAAAGGAGAAGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGG
|
|
3
|
+
+
|
|
4
|
+
Zb^Ld`N\[d`NaZ[aZc]UOKGB;[\YT[_W[aZ\aZ[Zd`SE_WeaUH[Y\[[\\\[\Z\aY`X[[aZ\aZ\d`OY[aY[[\[[e`WPJ@^UZ[`X\[R]T_V_W[`[Fa\H`\G[[Q^TVa\Ha\Hc^LY\S
|
|
5
|
+
@SRR014849.110027 EIXKN4201APUB0 length=131
|
|
6
|
+
CTTCAAATGATTCCGGGACTGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTTCGGTTCCAACTCGCCGTCCGAATAATCCGTTCAAAATCTTGGCCTGTCAAAACGACTTTACGACCAGAACGATCCG
|
|
7
|
+
+
|
|
8
|
+
\aYY_[EY\T`X^Vd`OY\[[^U_V[R^T[_ZBc^La\GYYO\S[c^Ld`Nc_Q;ZaZaYaY`XZZ\[aZZ[aZ[aZ[aZY`Z[`ZWeaVJ\[aZaY`X[PY\eaUF[\[[d`OXTUZ[Q\\`W\\\Y_W\
|
|
9
|
+
@SRR014849.203935 EIXKN4201B4HU6 length=144
|
|
10
|
+
AACCCGTCCCATCAAAGATTTTGGTTGGAACCCGAAAGGGTTTTGAATTCAAACCCCTTTCGGTTCCAACTATTCAATTGTTTAACTTTTTTTAAATTGATGGTCTGTTGGACCATTTGTAATAATCCCCATCGGAATTTCTTT
|
|
11
|
+
+
|
|
12
|
+
`Z_ZBVT^Y>[[Xd`PZ\d`RBaZaZ`ZaZ_ZBXd`Pd`Pd`RB[aZ`ZWd`Oc_R@d`P\aZ`ZaZaZY\YaZYaY`XYd`O`X[e`WPJC;c^LaZS[YYN[Z\Y`XWLT^U\b]JW[[RZ\SYc`RB[Z\WLXM`\GYa\H
|
metadata
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: bio-faster
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 0.
|
|
4
|
+
version: 0.4.2
|
|
5
5
|
prerelease:
|
|
6
6
|
platform: ruby
|
|
7
7
|
authors:
|
|
@@ -9,11 +9,22 @@ authors:
|
|
|
9
9
|
autorequire:
|
|
10
10
|
bindir: bin
|
|
11
11
|
cert_chain: []
|
|
12
|
-
date: 2012-04-
|
|
12
|
+
date: 2012-04-27 00:00:00.000000000 Z
|
|
13
13
|
dependencies:
|
|
14
|
+
- !ruby/object:Gem::Dependency
|
|
15
|
+
name: ffi
|
|
16
|
+
requirement: &2153396520 !ruby/object:Gem::Requirement
|
|
17
|
+
none: false
|
|
18
|
+
requirements:
|
|
19
|
+
- - ! '>='
|
|
20
|
+
- !ruby/object:Gem::Version
|
|
21
|
+
version: '0'
|
|
22
|
+
type: :runtime
|
|
23
|
+
prerelease: false
|
|
24
|
+
version_requirements: *2153396520
|
|
14
25
|
- !ruby/object:Gem::Dependency
|
|
15
26
|
name: shoulda
|
|
16
|
-
requirement: &
|
|
27
|
+
requirement: &2153396000 !ruby/object:Gem::Requirement
|
|
17
28
|
none: false
|
|
18
29
|
requirements:
|
|
19
30
|
- - ! '>='
|
|
@@ -21,10 +32,10 @@ dependencies:
|
|
|
21
32
|
version: '0'
|
|
22
33
|
type: :development
|
|
23
34
|
prerelease: false
|
|
24
|
-
version_requirements: *
|
|
35
|
+
version_requirements: *2153396000
|
|
25
36
|
- !ruby/object:Gem::Dependency
|
|
26
37
|
name: bundler
|
|
27
|
-
requirement: &
|
|
38
|
+
requirement: &2153395420 !ruby/object:Gem::Requirement
|
|
28
39
|
none: false
|
|
29
40
|
requirements:
|
|
30
41
|
- - ~>
|
|
@@ -32,10 +43,10 @@ dependencies:
|
|
|
32
43
|
version: 1.0.0
|
|
33
44
|
type: :development
|
|
34
45
|
prerelease: false
|
|
35
|
-
version_requirements: *
|
|
46
|
+
version_requirements: *2153395420
|
|
36
47
|
- !ruby/object:Gem::Dependency
|
|
37
48
|
name: jeweler
|
|
38
|
-
requirement: &
|
|
49
|
+
requirement: &2153394940 !ruby/object:Gem::Requirement
|
|
39
50
|
none: false
|
|
40
51
|
requirements:
|
|
41
52
|
- - ~>
|
|
@@ -43,10 +54,10 @@ dependencies:
|
|
|
43
54
|
version: 1.6.4
|
|
44
55
|
type: :development
|
|
45
56
|
prerelease: false
|
|
46
|
-
version_requirements: *
|
|
57
|
+
version_requirements: *2153394940
|
|
47
58
|
- !ruby/object:Gem::Dependency
|
|
48
59
|
name: rcov
|
|
49
|
-
requirement: &
|
|
60
|
+
requirement: &2153394460 !ruby/object:Gem::Requirement
|
|
50
61
|
none: false
|
|
51
62
|
requirements:
|
|
52
63
|
- - ! '>='
|
|
@@ -54,10 +65,10 @@ dependencies:
|
|
|
54
65
|
version: '0'
|
|
55
66
|
type: :development
|
|
56
67
|
prerelease: false
|
|
57
|
-
version_requirements: *
|
|
68
|
+
version_requirements: *2153394460
|
|
58
69
|
- !ruby/object:Gem::Dependency
|
|
59
70
|
name: bio
|
|
60
|
-
requirement: &
|
|
71
|
+
requirement: &2153393980 !ruby/object:Gem::Requirement
|
|
61
72
|
none: false
|
|
62
73
|
requirements:
|
|
63
74
|
- - ! '>='
|
|
@@ -65,10 +76,21 @@ dependencies:
|
|
|
65
76
|
version: 1.4.2
|
|
66
77
|
type: :development
|
|
67
78
|
prerelease: false
|
|
68
|
-
version_requirements: *
|
|
79
|
+
version_requirements: *2153393980
|
|
69
80
|
- !ruby/object:Gem::Dependency
|
|
70
81
|
name: rspec
|
|
71
|
-
requirement: &
|
|
82
|
+
requirement: &2153409780 !ruby/object:Gem::Requirement
|
|
83
|
+
none: false
|
|
84
|
+
requirements:
|
|
85
|
+
- - ! '>='
|
|
86
|
+
- !ruby/object:Gem::Version
|
|
87
|
+
version: '0'
|
|
88
|
+
type: :development
|
|
89
|
+
prerelease: false
|
|
90
|
+
version_requirements: *2153409780
|
|
91
|
+
- !ruby/object:Gem::Dependency
|
|
92
|
+
name: ffi
|
|
93
|
+
requirement: &2153409260 !ruby/object:Gem::Requirement
|
|
72
94
|
none: false
|
|
73
95
|
requirements:
|
|
74
96
|
- - ! '>='
|
|
@@ -76,12 +98,12 @@ dependencies:
|
|
|
76
98
|
version: '0'
|
|
77
99
|
type: :development
|
|
78
100
|
prerelease: false
|
|
79
|
-
version_requirements: *
|
|
80
|
-
description: A fast parser for
|
|
101
|
+
version_requirements: *2153409260
|
|
102
|
+
description: A fast parser for FastQ files
|
|
81
103
|
email: francesco.strozzi@gmail.com
|
|
82
104
|
executables: []
|
|
83
105
|
extensions:
|
|
84
|
-
- ext/
|
|
106
|
+
- ext/mkrf_conf.rb
|
|
85
107
|
extra_rdoc_files:
|
|
86
108
|
- LICENSE.txt
|
|
87
109
|
- README.md
|
|
@@ -95,16 +117,55 @@ files:
|
|
|
95
117
|
- Rakefile
|
|
96
118
|
- VERSION
|
|
97
119
|
- bio-faster.gemspec
|
|
98
|
-
- ext/extconf.rb
|
|
99
120
|
- ext/faster.c
|
|
100
|
-
- ext/
|
|
121
|
+
- ext/mkrf_conf.rb
|
|
101
122
|
- lib/bio-faster.rb
|
|
123
|
+
- lib/bio/faster.rb
|
|
124
|
+
- lib/bio/faster/library.rb
|
|
125
|
+
- spec/fastq_error_spec.rb
|
|
102
126
|
- spec/helper.rb
|
|
103
127
|
- spec/parser_spec.rb
|
|
104
|
-
- test/data/
|
|
105
|
-
- test/data/
|
|
106
|
-
- test/data/
|
|
107
|
-
- test/data/
|
|
128
|
+
- test/data/errors/error_header.fastq
|
|
129
|
+
- test/data/errors/error_long_qual.fastq
|
|
130
|
+
- test/data/errors/error_qual_del.fastq
|
|
131
|
+
- test/data/errors/error_qual_escape.fastq
|
|
132
|
+
- test/data/errors/error_qual_null.fastq
|
|
133
|
+
- test/data/errors/error_qual_space.fastq
|
|
134
|
+
- test/data/errors/error_qual_tab.fastq
|
|
135
|
+
- test/data/errors/error_qual_unit_sep.fastq
|
|
136
|
+
- test/data/errors/error_qual_vtab.fastq
|
|
137
|
+
- test/data/errors/error_spaces.fastq
|
|
138
|
+
- test/data/errors/error_tabs.fastq
|
|
139
|
+
- test/data/errors/error_trunc_at_qual.fastq
|
|
140
|
+
- test/data/errors/error_trunc_at_seq.fastq
|
|
141
|
+
- test/data/errors/error_trunc_in_qual.fastq
|
|
142
|
+
- test/data/errors/error_trunc_in_seq.fastq
|
|
143
|
+
- test/data/formats/illumina_full_range_as_illumina.fastq
|
|
144
|
+
- test/data/formats/illumina_full_range_as_sanger.fastq
|
|
145
|
+
- test/data/formats/illumina_full_range_as_solexa.fastq
|
|
146
|
+
- test/data/formats/illumina_full_range_original_illumina.fastq
|
|
147
|
+
- test/data/formats/longreads_as_illumina.fastq
|
|
148
|
+
- test/data/formats/longreads_as_sanger.fastq
|
|
149
|
+
- test/data/formats/longreads_as_solexa.fastq
|
|
150
|
+
- test/data/formats/misc_dna_as_illumina.fastq
|
|
151
|
+
- test/data/formats/misc_dna_as_sanger.fastq
|
|
152
|
+
- test/data/formats/misc_dna_as_solexa.fastq
|
|
153
|
+
- test/data/formats/misc_dna_original_sanger.fastq
|
|
154
|
+
- test/data/formats/misc_rna_as_illumina.fastq
|
|
155
|
+
- test/data/formats/misc_rna_as_sanger.fastq
|
|
156
|
+
- test/data/formats/misc_rna_as_solexa.fastq
|
|
157
|
+
- test/data/formats/misc_rna_original_sanger.fastq
|
|
158
|
+
- test/data/formats/sanger_full_range_as_illumina.fastq
|
|
159
|
+
- test/data/formats/sanger_full_range_as_sanger.fastq
|
|
160
|
+
- test/data/formats/sanger_full_range_as_solexa.fastq
|
|
161
|
+
- test/data/formats/sanger_full_range_original_sanger.fastq
|
|
162
|
+
- test/data/formats/solexa_full_range_as_illumina.fastq
|
|
163
|
+
- test/data/formats/solexa_full_range_as_sanger.fastq
|
|
164
|
+
- test/data/formats/solexa_full_range_as_solexa.fastq
|
|
165
|
+
- test/data/formats/solexa_full_range_original_solexa.fastq
|
|
166
|
+
- test/data/formats/wrapping_as_illumina.fastq
|
|
167
|
+
- test/data/formats/wrapping_as_sanger.fastq
|
|
168
|
+
- test/data/formats/wrapping_as_solexa.fastq
|
|
108
169
|
homepage: http://github.com/fstrozzi/bioruby-faster
|
|
109
170
|
licenses:
|
|
110
171
|
- MIT
|
|
@@ -117,7 +178,10 @@ required_ruby_version: !ruby/object:Gem::Requirement
|
|
|
117
178
|
requirements:
|
|
118
179
|
- - ! '>='
|
|
119
180
|
- !ruby/object:Gem::Version
|
|
120
|
-
version: '
|
|
181
|
+
version: '0'
|
|
182
|
+
segments:
|
|
183
|
+
- 0
|
|
184
|
+
hash: 4125702484128053207
|
|
121
185
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
|
122
186
|
none: false
|
|
123
187
|
requirements:
|
|
@@ -129,5 +193,5 @@ rubyforge_project:
|
|
|
129
193
|
rubygems_version: 1.8.15
|
|
130
194
|
signing_key:
|
|
131
195
|
specification_version: 3
|
|
132
|
-
summary: A fast parser for
|
|
196
|
+
summary: A fast parser for FastQ files
|
|
133
197
|
test_files: []
|
data/ext/extconf.rb
DELETED
data/ext/kseq.h
DELETED
|
@@ -1,223 +0,0 @@
|
|
|
1
|
-
/* The MIT License
|
|
2
|
-
|
|
3
|
-
Copyright (c) 2008 Genome Research Ltd (GRL).
|
|
4
|
-
|
|
5
|
-
Permission is hereby granted, free of charge, to any person obtaining
|
|
6
|
-
a copy of this software and associated documentation files (the
|
|
7
|
-
"Software"), to deal in the Software without restriction, including
|
|
8
|
-
without limitation the rights to use, copy, modify, merge, publish,
|
|
9
|
-
distribute, sublicense, and/or sell copies of the Software, and to
|
|
10
|
-
permit persons to whom the Software is furnished to do so, subject to
|
|
11
|
-
the following conditions:
|
|
12
|
-
|
|
13
|
-
The above copyright notice and this permission notice shall be
|
|
14
|
-
included in all copies or substantial portions of the Software.
|
|
15
|
-
|
|
16
|
-
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
|
17
|
-
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
|
|
18
|
-
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
|
19
|
-
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
|
|
20
|
-
BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
|
|
21
|
-
ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
|
|
22
|
-
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
|
|
23
|
-
SOFTWARE.
|
|
24
|
-
*/
|
|
25
|
-
|
|
26
|
-
/* Contact: Heng Li <lh3@sanger.ac.uk> */
|
|
27
|
-
|
|
28
|
-
/* Last Modified: 12APR2009 */
|
|
29
|
-
|
|
30
|
-
#ifndef AC_KSEQ_H
|
|
31
|
-
#define AC_KSEQ_H
|
|
32
|
-
|
|
33
|
-
#include <ctype.h>
|
|
34
|
-
#include <string.h>
|
|
35
|
-
#include <stdlib.h>
|
|
36
|
-
|
|
37
|
-
#define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r
|
|
38
|
-
#define KS_SEP_TAB 1 // isspace() && !' '
|
|
39
|
-
#define KS_SEP_MAX 1
|
|
40
|
-
|
|
41
|
-
#define __KS_TYPE(type_t) \
|
|
42
|
-
typedef struct __kstream_t { \
|
|
43
|
-
char *buf; \
|
|
44
|
-
int begin, end, is_eof; \
|
|
45
|
-
type_t f; \
|
|
46
|
-
} kstream_t;
|
|
47
|
-
|
|
48
|
-
#define ks_eof(ks) ((ks)->is_eof && (ks)->begin >= (ks)->end)
|
|
49
|
-
#define ks_rewind(ks) ((ks)->is_eof = (ks)->begin = (ks)->end = 0)
|
|
50
|
-
|
|
51
|
-
#define __KS_BASIC(type_t, __bufsize) \
|
|
52
|
-
static inline kstream_t *ks_init(type_t f) \
|
|
53
|
-
{ \
|
|
54
|
-
kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t)); \
|
|
55
|
-
ks->f = f; \
|
|
56
|
-
ks->buf = (char*)malloc(__bufsize); \
|
|
57
|
-
return ks; \
|
|
58
|
-
} \
|
|
59
|
-
static inline void ks_destroy(kstream_t *ks) \
|
|
60
|
-
{ \
|
|
61
|
-
if (ks) { \
|
|
62
|
-
free(ks->buf); \
|
|
63
|
-
free(ks); \
|
|
64
|
-
} \
|
|
65
|
-
}
|
|
66
|
-
|
|
67
|
-
#define __KS_GETC(__read, __bufsize) \
|
|
68
|
-
static inline int ks_getc(kstream_t *ks) \
|
|
69
|
-
{ \
|
|
70
|
-
if (ks->is_eof && ks->begin >= ks->end) return -1; \
|
|
71
|
-
if (ks->begin >= ks->end) { \
|
|
72
|
-
ks->begin = 0; \
|
|
73
|
-
ks->end = __read(ks->f, ks->buf, __bufsize); \
|
|
74
|
-
if (ks->end < __bufsize) ks->is_eof = 1; \
|
|
75
|
-
if (ks->end == 0) return -1; \
|
|
76
|
-
} \
|
|
77
|
-
return (int)ks->buf[ks->begin++]; \
|
|
78
|
-
}
|
|
79
|
-
|
|
80
|
-
#ifndef KSTRING_T
|
|
81
|
-
#define KSTRING_T kstring_t
|
|
82
|
-
typedef struct __kstring_t {
|
|
83
|
-
size_t l, m;
|
|
84
|
-
char *s;
|
|
85
|
-
} kstring_t;
|
|
86
|
-
#endif
|
|
87
|
-
|
|
88
|
-
#ifndef kroundup32
|
|
89
|
-
#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
|
|
90
|
-
#endif
|
|
91
|
-
|
|
92
|
-
#define __KS_GETUNTIL(__read, __bufsize) \
|
|
93
|
-
static int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \
|
|
94
|
-
{ \
|
|
95
|
-
if (dret) *dret = 0; \
|
|
96
|
-
str->l = 0; \
|
|
97
|
-
if (ks->begin >= ks->end && ks->is_eof) return -1; \
|
|
98
|
-
for (;;) { \
|
|
99
|
-
int i; \
|
|
100
|
-
if (ks->begin >= ks->end) { \
|
|
101
|
-
if (!ks->is_eof) { \
|
|
102
|
-
ks->begin = 0; \
|
|
103
|
-
ks->end = __read(ks->f, ks->buf, __bufsize); \
|
|
104
|
-
if (ks->end < __bufsize) ks->is_eof = 1; \
|
|
105
|
-
if (ks->end == 0) break; \
|
|
106
|
-
} else break; \
|
|
107
|
-
} \
|
|
108
|
-
if (delimiter > KS_SEP_MAX) { \
|
|
109
|
-
for (i = ks->begin; i < ks->end; ++i) \
|
|
110
|
-
if (ks->buf[i] == delimiter) break; \
|
|
111
|
-
} else if (delimiter == KS_SEP_SPACE) { \
|
|
112
|
-
for (i = ks->begin; i < ks->end; ++i) \
|
|
113
|
-
if (isspace(ks->buf[i])) break; \
|
|
114
|
-
} else if (delimiter == KS_SEP_TAB) { \
|
|
115
|
-
for (i = ks->begin; i < ks->end; ++i) \
|
|
116
|
-
if (isspace(ks->buf[i]) && ks->buf[i] != ' ') break; \
|
|
117
|
-
} else i = 0; /* never come to here! */ \
|
|
118
|
-
if (str->m - str->l < i - ks->begin + 1) { \
|
|
119
|
-
str->m = str->l + (i - ks->begin) + 1; \
|
|
120
|
-
kroundup32(str->m); \
|
|
121
|
-
str->s = (char*)realloc(str->s, str->m); \
|
|
122
|
-
} \
|
|
123
|
-
memcpy(str->s + str->l, ks->buf + ks->begin, i - ks->begin); \
|
|
124
|
-
str->l = str->l + (i - ks->begin); \
|
|
125
|
-
ks->begin = i + 1; \
|
|
126
|
-
if (i < ks->end) { \
|
|
127
|
-
if (dret) *dret = ks->buf[i]; \
|
|
128
|
-
break; \
|
|
129
|
-
} \
|
|
130
|
-
} \
|
|
131
|
-
if (str->l == 0) { \
|
|
132
|
-
str->m = 1; \
|
|
133
|
-
str->s = (char*)calloc(1, 1); \
|
|
134
|
-
} \
|
|
135
|
-
str->s[str->l] = '\0'; \
|
|
136
|
-
return str->l; \
|
|
137
|
-
}
|
|
138
|
-
|
|
139
|
-
#define KSTREAM_INIT(type_t, __read, __bufsize) \
|
|
140
|
-
__KS_TYPE(type_t) \
|
|
141
|
-
__KS_BASIC(type_t, __bufsize) \
|
|
142
|
-
__KS_GETC(__read, __bufsize) \
|
|
143
|
-
__KS_GETUNTIL(__read, __bufsize)
|
|
144
|
-
|
|
145
|
-
#define __KSEQ_BASIC(type_t) \
|
|
146
|
-
static inline kseq_t *kseq_init(type_t fd) \
|
|
147
|
-
{ \
|
|
148
|
-
kseq_t *s = (kseq_t*)calloc(1, sizeof(kseq_t)); \
|
|
149
|
-
s->f = ks_init(fd); \
|
|
150
|
-
return s; \
|
|
151
|
-
} \
|
|
152
|
-
static inline void kseq_rewind(kseq_t *ks) \
|
|
153
|
-
{ \
|
|
154
|
-
ks->last_char = 0; \
|
|
155
|
-
ks->f->is_eof = ks->f->begin = ks->f->end = 0; \
|
|
156
|
-
} \
|
|
157
|
-
static inline void kseq_destroy(kseq_t *ks) \
|
|
158
|
-
{ \
|
|
159
|
-
if (!ks) return; \
|
|
160
|
-
free(ks->name.s); free(ks->comment.s); free(ks->seq.s); free(ks->qual.s); \
|
|
161
|
-
ks_destroy(ks->f); \
|
|
162
|
-
free(ks); \
|
|
163
|
-
}
|
|
164
|
-
|
|
165
|
-
/* Return value:
|
|
166
|
-
>=0 length of the sequence (normal)
|
|
167
|
-
-1 end-of-file
|
|
168
|
-
-2 truncated quality string
|
|
169
|
-
*/
|
|
170
|
-
#define __KSEQ_READ \
|
|
171
|
-
static int kseq_read(kseq_t *seq) \
|
|
172
|
-
{ \
|
|
173
|
-
int c; \
|
|
174
|
-
kstream_t *ks = seq->f; \
|
|
175
|
-
if (seq->last_char == 0) { /* then jump to the next header line */ \
|
|
176
|
-
while ((c = ks_getc(ks)) != -1 && c != '>' && c != '@'); \
|
|
177
|
-
if (c == -1) return -1; /* end of file */ \
|
|
178
|
-
seq->last_char = c; \
|
|
179
|
-
} /* the first header char has been read */ \
|
|
180
|
-
seq->comment.l = seq->seq.l = seq->qual.l = 0; \
|
|
181
|
-
if (ks_getuntil(ks, 0, &seq->name, &c) < 0) return -1; \
|
|
182
|
-
if (c != '\n') ks_getuntil(ks, '\n', &seq->comment, 0); \
|
|
183
|
-
while ((c = ks_getc(ks)) != -1 && c != '>' && c != '+' && c != '@') { \
|
|
184
|
-
if (isgraph(c)) { /* printable non-space character */ \
|
|
185
|
-
if (seq->seq.l + 1 >= seq->seq.m) { /* double the memory */ \
|
|
186
|
-
seq->seq.m = seq->seq.l + 2; \
|
|
187
|
-
kroundup32(seq->seq.m); /* rounded to next closest 2^k */ \
|
|
188
|
-
seq->seq.s = (char*)realloc(seq->seq.s, seq->seq.m); \
|
|
189
|
-
} \
|
|
190
|
-
seq->seq.s[seq->seq.l++] = (char)c; \
|
|
191
|
-
} \
|
|
192
|
-
} \
|
|
193
|
-
if (c == '>' || c == '@') seq->last_char = c; /* the first header char has been read */ \
|
|
194
|
-
seq->seq.s[seq->seq.l] = 0; /* null terminated string */ \
|
|
195
|
-
if (c != '+') return seq->seq.l; /* FASTA */ \
|
|
196
|
-
if (seq->qual.m < seq->seq.m) { /* allocate enough memory */ \
|
|
197
|
-
seq->qual.m = seq->seq.m; \
|
|
198
|
-
seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m); \
|
|
199
|
-
} \
|
|
200
|
-
while ((c = ks_getc(ks)) != -1 && c != '\n'); /* skip the rest of '+' line */ \
|
|
201
|
-
if (c == -1) return -2; /* we should not stop here */ \
|
|
202
|
-
while ((c = ks_getc(ks)) != -1 && seq->qual.l < seq->seq.l) \
|
|
203
|
-
if (c >= 33 && c <= 127) seq->qual.s[seq->qual.l++] = (unsigned char)c; \
|
|
204
|
-
seq->qual.s[seq->qual.l] = 0; /* null terminated string */ \
|
|
205
|
-
seq->last_char = 0; /* we have not come to the next header line */ \
|
|
206
|
-
if (seq->seq.l != seq->qual.l) return -2; /* qual string is shorter than seq string */ \
|
|
207
|
-
return seq->seq.l; \
|
|
208
|
-
}
|
|
209
|
-
|
|
210
|
-
#define __KSEQ_TYPE(type_t) \
|
|
211
|
-
typedef struct { \
|
|
212
|
-
kstring_t name, comment, seq, qual; \
|
|
213
|
-
int last_char; \
|
|
214
|
-
kstream_t *f; \
|
|
215
|
-
} kseq_t;
|
|
216
|
-
|
|
217
|
-
#define KSEQ_INIT(type_t, __read) \
|
|
218
|
-
KSTREAM_INIT(type_t, __read, 4096) \
|
|
219
|
-
__KSEQ_TYPE(type_t) \
|
|
220
|
-
__KSEQ_BASIC(type_t) \
|
|
221
|
-
__KSEQ_READ
|
|
222
|
-
|
|
223
|
-
#endif
|