bio-faster 0.2.2 → 0.4.2
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- 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
|
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|
|
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requirements:
|
|
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- - ! '>='
|
|
@@ -21,10 +32,10 @@ dependencies:
|
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|
version: '0'
|
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type: :development
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|
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|
prerelease: false
|
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version_requirements: *
|
|
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|
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|
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name: bundler
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requirement: &
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requirements:
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|
- - ~>
|
|
@@ -32,10 +43,10 @@ dependencies:
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|
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name: jeweler
|
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requirement: &
|
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|
+
requirement: &2153394940 !ruby/object:Gem::Requirement
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|
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requirements:
|
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|
- - ~>
|
|
@@ -43,10 +54,10 @@ dependencies:
|
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|
version: 1.6.4
|
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|
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|
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|
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name: rcov
|
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requirement: &
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|
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requirement: &2153394460 !ruby/object:Gem::Requirement
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|
|
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requirements:
|
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|
- - ! '>='
|
|
@@ -54,10 +65,10 @@ dependencies:
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|
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|
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|
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|
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|
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|
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|
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|
- !ruby/object:Gem::Dependency
|
|
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|
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|
|
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|
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requirement: &2153393980 !ruby/object:Gem::Requirement
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|
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|
- - ! '>='
|
|
@@ -65,10 +76,21 @@ dependencies:
|
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|
version: 1.4.2
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version_requirements: *
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|
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|
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name: rspec
|
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|
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requirement: &2153409780 !ruby/object:Gem::Requirement
|
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none: false
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|
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requirements:
|
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|
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- - ! '>='
|
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|
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- !ruby/object:Gem::Version
|
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|
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version: '0'
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type: :development
|
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|
+
prerelease: false
|
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|
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version_requirements: *2153409780
|
|
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|
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- !ruby/object:Gem::Dependency
|
|
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|
+
name: ffi
|
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|
|
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|
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|
|
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|
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|
|
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|
- - ! '>='
|
|
@@ -76,12 +98,12 @@ dependencies:
|
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|
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|
|
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|
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|
|
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|
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|
|
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|
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version_requirements: *
|
|
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|
-
description: A fast parser for
|
|
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|
+
version_requirements: *2153409260
|
|
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|
+
description: A fast parser for FastQ files
|
|
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103
|
email: francesco.strozzi@gmail.com
|
|
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|
executables: []
|
|
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|
extensions:
|
|
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|
-
- ext/
|
|
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|
+
- ext/mkrf_conf.rb
|
|
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|
extra_rdoc_files:
|
|
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|
- LICENSE.txt
|
|
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109
|
- README.md
|
|
@@ -95,16 +117,55 @@ files:
|
|
|
95
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|
- Rakefile
|
|
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|
- VERSION
|
|
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|
- bio-faster.gemspec
|
|
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|
-
- ext/extconf.rb
|
|
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120
|
- ext/faster.c
|
|
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|
-
- ext/
|
|
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|
+
- ext/mkrf_conf.rb
|
|
101
122
|
- lib/bio-faster.rb
|
|
123
|
+
- lib/bio/faster.rb
|
|
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|
+
- lib/bio/faster/library.rb
|
|
125
|
+
- spec/fastq_error_spec.rb
|
|
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126
|
- spec/helper.rb
|
|
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|
- spec/parser_spec.rb
|
|
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|
-
- test/data/
|
|
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|
-
- test/data/
|
|
106
|
-
- test/data/
|
|
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|
-
- test/data/
|
|
128
|
+
- test/data/errors/error_header.fastq
|
|
129
|
+
- test/data/errors/error_long_qual.fastq
|
|
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|
+
- test/data/errors/error_qual_del.fastq
|
|
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|
+
- test/data/errors/error_qual_escape.fastq
|
|
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|
+
- test/data/errors/error_qual_null.fastq
|
|
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|
+
- test/data/errors/error_qual_space.fastq
|
|
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|
+
- test/data/errors/error_qual_tab.fastq
|
|
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|
+
- test/data/errors/error_qual_unit_sep.fastq
|
|
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|
+
- 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
|
|
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|
+
- 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
|
|
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|
+
- test/data/formats/illumina_full_range_as_illumina.fastq
|
|
144
|
+
- test/data/formats/illumina_full_range_as_sanger.fastq
|
|
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|
+
- 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
|
|
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|
+
- test/data/formats/sanger_full_range_as_solexa.fastq
|
|
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|
+
- test/data/formats/sanger_full_range_original_sanger.fastq
|
|
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|
+
- 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
|
|
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|
+
- 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
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|
requirements:
|
|
118
179
|
- - ! '>='
|
|
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|
- !ruby/object:Gem::Version
|
|
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|
-
version: '
|
|
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|
+
version: '0'
|
|
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|
+
segments:
|
|
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|
+
- 0
|
|
184
|
+
hash: 4125702484128053207
|
|
121
185
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
|
122
186
|
none: false
|
|
123
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|
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
|