forked from rhythms06/repseqio
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathCHANGELOG
168 lines (108 loc) · 5.09 KB
/
CHANGELOG
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
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
Changelog for later versions available at:
https://github.com/repseqio/repseqio/releases
RepSeqIO 1.3.4 (15 Apr 2020)
========================
-- Bug fix in method for retrieving coding gene feature
-- Update for library v1.6
RepSeqIO 1.3.3 (19 Nov 2019)
========================
-- Internal library upgraded to RepSeq.IO v1.6
-- Better error when CDR3 contains wildcards (pull-request #42 from @bbimber)
-- Minor optimizations for HTTP sequence resolver
-- Better endpoint for NCBI's nuccore sequence retrieval
-- Fixes for `compile` action with small base sequences
RepSeqIO 1.3.2 (22 Jul 2019)
========================
-- Fix for empty `Chains` JSON serialization
-- Some new `Chains` constants
RepSeqIO 1.3.1 (30 Jan 2019)
========================
-- MiLib ubgrade to 1.10
RepSeqIO 1.3 (23 Oct 2018)
========================
-- JDK 8
-- Minor library resolution logic corrections.
-- Migration to new library versions (MiLib, Jeckson)
RepSeqIO 1.2.12 (14 Jun 2018)
========================
-- Added allele name to TsvAction (#41) [@bbimber]
RepSeqIO 1.2.11 ( 7 Feb 2018)
========================
-- Built-in library upgraded to 1.5, many genes updated / added (see library changelog for
modifications)
-- Major refactoring of `fromPaddedFasta` action, separate action for plain fasta import (see
`fromFasta`). Convenient pipeline for importing fasta files (see README)
-- Added GeneFeature#isAlignmentAttached() method
-- minor: Fix for incorrect negative value interpretation in `fromPaddedFasta` action
-- minor: several other minor enhancements
RepSeqIO 1.2.10 (24 Jul 2017)
========================
-- Update to MiLib 1.8.1
RepSeqIO 1.2.9 (24 Jul 2017)
========================
RepSeqIO 1.2.8 ( 7 Jun 2017)
========================
-- Artificial repertoire generator (user defined model, built-in model for TRB rearengements from
*Murugan et al., 2012*; use model name `murugan`)
-- Infrastructure for artificial repretoire generation + possible format for description of V(D)J
rearengements (`*.jclns`)
-- Fixed method `VDJGene#getFamilyName`
-- Added Chains#parse method
-- Two implementations for `ReferencePoints` (normal and extended - used in artificial `GClone`s)
-- `isComplete()` method for `VDJGene`
-- Two convenient `getGenes` method variants for `VDJCLibrary`
-- Information about build host now is added to output binary jar file
RepSeqIO 1.2.7 ( 2 Mar 2017)
========================
-- New action `tsv` to export library content to tab-delimited table (pull-request from @bbimber)
-- Added more validations for `debug` action (pull-request from @bbimber)
-- Warning messages for `inferPoints` action in case the inferred point doesn't match point from
target library (pull-request from @bbimber)
-- Fixed bug in `SequencePartitioning`, bug affected results of getRelativeRange for zero-length
gene features
-- (alpha) Support for notes in the library files
-- (alpha) Tags for individual genes
RepSeqIO 1.2.6 ( 4 Feb 2017)
========================
-- Additional modification to `io.repseq.core.GeneFeature#intersection`. Split into two methods
`intersection` and `intersectionStrict`.
-- `getSafe()` method added to VDJCGene class
RepSeqIO 1.2.5 (30 Jan 2017)
========================
-- Added alias anchor point `DRegionTrimmed` = `DCDR3Part`
-- Fix for wrong behaviour of `io.repseq.core.GeneFeature#intersection` for gene features with two
P segments (like D gene with both right and left P segment)
-- minor: NPE in getRelativeRange with PSergments fixed
RepSeqIO 1.2.4 (26 Dec 2016)
========================
-- Explicit warning messages in `debug` action (thanks to @bbimber).
-- New checks in `debug` action (thanks to @bbimber): intron splice site validation, etc...
-- Added `getTranslationParameters(...)` in `SequencePartitioning`, unified way to infer
translation frame for given gene feature
-- Added `getCodingFeature` in `GeneFeature`, extracts coding sub-feature from given gene feature
-- Internal library updated to v1.2 (added rat reference, fix for human TRAJ55 pseudogene)
-- minor: Fix for space in io.repseq.core.GeneFeature#encode
RepSeqIO 1.2.3 ( 7 Dec 2016)
========================
-- Support for Linux `free` version 3.3.10 in `repseqio` wrapper script (now RepSeq.io runs on
Centos 7.2, Ubuntu 16.04.1)
RepSeqIO 1.2.2 ( 8 Nov 2016)
========================
-- Fixes IO exception if library search folder not exists
-- `loadAllLibraries` method in `VDJCLibraryRegistry`
-- `LibraryNameListProvider` interface for library resolvers
-- Reverse species name search in `VDJCLibraryRegistry`
-- Built-in library updated to v1.1 (fixed human IGHV4-61 and IGLC7, IGLC3)
-- NCBI sequence resolver now works over https
-- Additional sequence id extractor for new NCBI naming convention
RepSeqIO 1.2.1 ( 7 Oct 2016)
========================
-- Fixes bug when FolderResolver fails to resolve partial library name for files without .gz
-- Fixes bug not allowing to inferPoints using built-in library
RepSeqIO 1.2.0 (13 Sep 2016)
========================
RepSeqIO 1.1.0 (19 Aug 2016)
========================
RepSeqIO 1.0.0 (18 Jul 2016)
========================
-- First version