-
Notifications
You must be signed in to change notification settings - Fork 11
/
Copy pathChangelog
132 lines (103 loc) · 2.92 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
1.7.4
---
* Bugfix: Fix MAC calculation for non-binary (diploid_int, int) genotypes
1.7.3
---
* Bugfix: Correct figure label for FDR
1.7.2
--
* Enhancement: Users can specifiy if the chromosome should be colored in different colors and which fdr threshold to include in the Manhattan plots
1.7.1
--
* Bugfix: loading a gwas result from csv will properly check if it contains pvalues or scores
1.7.0
--
* Enhancement: Add support to transform phenotypes from the CLI
* Enhancement: Allow to specifiy transformation when calculating statistics
* Enhancement: Apply transformation before running GWAS when specified
1.6.1
--
* Bugfix: Fix QQ plotting function
1.6.0
--
* Enhancement: Better Manhattan plots (bigger marker sizes and better colors)
1.5.0
--
* Enhancement: Support for passing multiple candidate gene list files added
1.4.0
--
* Enhancement: Support for simple enrichment analysis added
1.3.1
--
* Bugfix: Make sure to properly cycle chromosome colors when plotting
* Bugfix: Make sure to convert scores to pvalues when loading a CSV GWAS result
* Bugfix: Return correct chromosomes for genotypes that don't start with Chr1
1.3.0
--
* Enhancement: Added functionality to generating QQ-Plots was added
1.2.1
--
* Bugfix: Deal with genotypes that have the chromosome as integer array instead of string array.
1.2.0
--
* Enhancement: Kinship matrix can be generated from the command line now
1.1.2
--
* Removed ipdb import
1.1.1
--
* Bugfix: Load GWAS result even if quantile and statistics are missing
* Bugfix: Allow to pass in a phenotype object instead of a phenotype file to calculate_stats function
1.1.0
--
* Support for calculating LD added
1.0.2
--
* Change: Remove hardcoded chromosomes names
1.0.1
--
* Bugfix: Plotting will make axis high enough to display the FDR threshold
* Bugfix: math domain error due to very low pvalues fixed
1.0.0
--
* Simplified command line args
* Fixed bug when plotting Manhattan plots that contain no data
0.1.10
--
* Remove hardcoded chromosome list
0.1.9
--
* Support for statistics (pseudo_heritability and shapiro wilks) added
* Bugfix regarding genotype.get_snp_at and genotype.get_snps_from_pos added
* Initial unit tests added
0.1.8
--
* Support for CSV files added.
* ArgumentParser supports now 3 sub commands (plot, convert and run)
* Plotting works with both CSV and HDF5 files
0.1.7
--
* Some Bugfixes when attribute (max_score, etc) are named differently
* Deal with GWAS results that don't have macs dataset
0.1.6
--
* Added dependency to matplitlib > 1.4.3 to fix plotting issue
0.1.5
--
* Added plotting module for plotting manhattan plots and also created plotter.py console script
0.1.4
--
* Improved performance of save_as_csv
* Improvied performance of snp_iterator and filter_non_binary function
* Some Bugfixes
0.1.3
--
* Fixed the setup (include files)
0.1.2
--
* Some bugfixes
* Proper support for calculating kinship
* Allows arbitary chunk_size for HDF5Genotype
0.1.0
--
* Initial release