forked from PeeperLab/CopywriteR
-
Notifications
You must be signed in to change notification settings - Fork 0
/
NEWS
88 lines (58 loc) · 2.76 KB
/
NEWS
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
Changes in version 2.0.6 (2015-06-15)
o Fixed another bug resulting from checking whether all co-analyzed bams were mapped to the same reference genome
-------------------------------------
Changes in version 2.0.5 (2015-06-10)
o Fixed an error resulting from checking whether all co-analyzed bams were mapped to the same reference genome
-------------------------------------
Changes in version 2.0.4 (2015-06-05)
o Fixed an error in plotCNA leading to mixing of chromosomes during plotting
-------------------------------------
Changes in version 2.0.3 (2015-05-06)
o Included MAD-values in CopywriteR log file
-------------------------------------
Changes in version 2.0.2 (2015-04-24)
o Fixed the bug that under certain circumstances error messages are thrown that .bam files are not coordinate sorted
-------------------------------------
Changes in version 2.0.1 (2015-04-18)
o Implemented resetting the original work directory upon exit of CopywriteR functions
o Corrected R dependency to version 3.2
o Updated DESCRIPTION file
o Fixed bug resulting in failure to calculate loesses
-------------------------------------
RELEASE (version 2.0)
-------------------------------------
Changes in version 1.99.4 (2015-04-08)
o Fixed bug related to logging when .bam are not indexed
-------------------------------------
Changes in version 1.99.3 (2015-04-06)
o Fixed bug related to testing of sort mode of .bam files
-------------------------------------
Changes in version 1.99.2 (2015-03-21)
o Provided vignette that allows R CMD CHECK --no-build-vignettes in <5 min
o Fixed minor bug affecting runs in which not all samples are analyzed by CopywriteR function
o Included a test for sorting of .bam files
o Improved error messages
o Fixed minor bug affecting plotting of samples
o Fixed minor bug causing error when processing >100 samples simultaneously
o Added support for capture regions bed files lacking the correct chromosome name prefix
o Fixed minor bug affecting read count statistics on single-sample analysis
-------------------------------------
Changes in version 1.99.0 (2015-03-05)
o Released new version
o Improved the speed of the package
o Implemented logging with the futile.logger package
o Replaced direct slot or field access with the use of accessor functions
o Implemented text wrapping
o Replaced the use of bed-file format with GRanges objects
o Created annotation and experiment packages
o Addressed all NOTES upon R CMD CHECK
o Restore options upon exit
o Adjusted version numbering to 1.99.0
o Implemented BiocParallel for parallel computing
o Changed name from ENCODER to CopywriteR
o Shortened lines to 80 characters
o Added NEWS file
o Changed F to FALSE
o Changed T to TRUE
o Added biocViews
o Changed version to 0.99.0