/
Changes
126 lines (82 loc) · 4.12 KB
/
Changes
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
{{$NEXT}}
2.0 2014-02-28 16:59:46EST-0500 EST5EDT
1.10 2014-02-28 16:55:28EST-0500 EST5EDT
* Removed dependency on forking and IO::Pipe for handling implicit
FASTA section starts. Should fix problems on Windows. Thanks to
Francisco Ossandon for the fix!
1.9 2014-01-20 13:05:18EST-0500 EST5EDT
* Added a check in the Parser to make sure that all lines that share
a single ID have the same type.
1.8 2013-10-28 10:57:26 EST5EDT
* Fixed a bug in which feature lines with no ID, Parent, or
Derives_from attributes were being returned as a bare hashref
instead of a single-element arrayref as they should be.
1.7 2013-10-02 15:49:40 EST5EDT
* Added `max_lookback` method to Parser, allowing applications to set
a maximum number of features to be stored in case they might be
referenced by features coming later in the file. Can make it
possible to parse GFF3 that does not contain enough '###'
directives.
1.6 2013-07-26 11:24:16 EST5EDT
* Improved the error message for when references between features
cannot be resolved. Instead of just Data::Dumper-ing the data
structure, prints a formatted report of which references could not
be resolved.
1.5 2012-12-14 12:40:58 America/New_York
* Added minimum Test::More version of 0.88 to tests.
1.4 2012-08-28 15:09:51 America/New_York
* Fix 1.0-backcompat crashing bug for GFF3 files with multi-location features.
1.3 2012-04-25 09:52:00 America/New_York
* Correct synopsis section of Bio::GFF3::LowLevel::Parser.
1.2 2012-04-13 17:47:29 America/New_York
* Removed unnecessary dependency on
Bio::GFF3::Transform::SyncDirectives that was causing installation
problems.
1.1 2012-04-13 01:32:21 America/New_York
* Changed the default API of Bio::GFF3::LowLevel::Parser to support
multi-loc features. In order to be able to group feature lines
that hand in some cases it would not be possibleave the same ID
attribute, it now returns arrayrefs that are groups of the
formerly-returned hashrefs.
* HOWEVER, there is a backward-compatibility layer that back-converts
the features to the conform to the return types in 1.1. Existing
users of this code should not be adversely affected.
* Add better support for Derives_from: feature line hashrefs now have
a derived_features attribute holding an arrayref of the features
that Derives_from this one.
* Remove assumptions in the parser about child features coming after
their parents in the file. The GFF3 specification does not require
this.
1.0 2012-03-21 00:51:41 America/Los_Angeles
* made parsing twice as fast as version 0.9, thanks to Devel::NYTProf
* fix bad bug with dropping the last few features in files with sync
directives
0.9 2012-03-20 20:26:04 America/Los_Angeles
* write the missing documentation
* make all features have child_features, for convenience
* strip whitespace from the end of comments before returning them
0.8 2012-03-20 17:24:50 America/Los_Angeles
* bugfix to handling of windows line-endings: parsers now remove them
regardless of the platform on which we are running.
* add gff3_parse_directive function to Bio::GFF3::LowLevel
0.7 2011-10-05 14:01:47 America/Los_Angeles
* when formatting GFF3 attributes, force ID, Name, Alias, and Parent
to be printed first.
0.6 2011-09-21 15:22:06 America/Los_Angeles
* when formatting GFF3 attributes, don't print attributes with no
value
0.5 2011-06-08 13:04:39 America/Los_Angeles
* tweak syncdirectives transform to hopefully work on win32
0.4 2011-04-26 14:45:29 America/Los_Angeles
* fix tests for older perls
0.3 2011-04-21 16:39:27 America/Los_Angeles
* fixed bug in SyncDirectives (gff3_insert_sync_directives)
transform, did not work if the file contained trailing tabs.
* added Bio::GFF3::Transform::FromFasta, which can make gff3 from
fasta
0.2 2011-03-08 15:43:01 America/New_York
* squash some warnings in LowLevel.pm
* add -i (in-place) option to gff3_insert_sync_directives
command-line script
0.01 2011-02-23 23:45 America/Los_Angeles
* initial release