-
Notifications
You must be signed in to change notification settings - Fork 3
/
CHANGES.txt
97 lines (64 loc) · 3.06 KB
/
CHANGES.txt
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
bioinf-commons changelog
===============
Here you can see the full list of changes between each release.
Version 0.0.9
-------------
Released on Apr 8, 2020
- Restructured codebase.
`org.jetbrains.bio.dataframe` - Pandas like dataframe
`org.jetbrains.bio.experiment` - Named computation - experiment and resources configuration
`org.jetbrains.bio.genome` - APIs for working with Genome, Sequence, Genes, Ontologies etc.
* `containers` - Genome location sets API
* `coverage` - Genome coverage API, paired/single end, fragment size estimation
* `data` - Describe any kind of dataset resources including replicates
* `format` - Bam (including Bisulfite sequencing), Bed, Fasta, Fastq, 2bit formats support
* `methylome` - API to work with methylomes - filtration, statistics, aggregations etc.
* `query` - Named functions - queries with caching capabilities
* `sampling` - API for genomic sampling - sequencies, locations, etc.
* `sequence` - Genome sequence API
Also: Biomart, Ensembl, UCSC support, Genomes and Genes annotations
`org.jetbrains.bio.statistics` - Statistics utilities including distributions mixtures, hmms and hypothesis testing
`org.jetbrains.bio.util` - Cancellable computations, progress reporters, logging utilities, and other utils
- Switched to SL4J and Logback for logging
Version 0.0.8
-------------
Released on Mar 3, 2020
- Removed non-generic code
Version 0.0.7
-------------
Released on October 23, 2019
- Added support for fitting regression mixtures / HMMs
- Added a mapability bigWig file to test data generation
- Changed the annotation configuration YAML structure: replaced "alias" field with "ucsc_alias" and "aliases",
which together with the build identifier form the "names" property.
Version 0.0.6
-------------
Released on XXXXXX
- `big` library upgraded to 0.9.0; corresponding code changes were made
- `BedFormat` dropped the `extraFieldsNumber` parameter, since it was never used anyway
- Consequently, the only type of BED format recognized from now on is `bedN+`
Version 0.0.5
-------------
Released on April 26, 2019
- Multistart support for `ClassificationModel`
- Reworked Genome object to support custom chromosomes sizes file
- BAM coverage improved support for ATAC-Seq files, fragment = 0
- Reduced iterations limit for EM algorithm
Version 0.0.4
-------------
Released on April 2, 2019
- Reduced default number of iterations and log likelihood threshold for faster statistical models convergence
- Improved `OptionParserExtensions` - show cmd line arguments in case of error
- `Classes` object removed
Version 0.0.3
-------------
Released on March 22, 2019
- Reworked `Genome` object configuration, by annotations file and naming conventions or explicitly
- Command line interfaces improvement - use `jline` library to detect actual terminal width
Version 0.0.2
-------------
Released on March 14, 2019
- Support all the chromosomes including contigs, random and alternative chromosomes in `GenomeQuery`
Version 0.0.1
-------------
Initial release, released on March 12, 2019