-
Notifications
You must be signed in to change notification settings - Fork 55
/
changelog.txt
130 lines (122 loc) · 7.95 KB
/
changelog.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
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
Version 1.8.3
- Updated submodule and version.
- Fixed check for introns for the case when deletion is next to insertion.
- Added PSTD flag description.
- Update Readme.md
- Updated changelog.txt
- Update Readme.md
- Updated integration tests to vcf 4.2
- Updated changelog.txt
- Updated version.
- Added validation of VCF files in integration tests. Fixed flag InDelLikely name in expected file and duplicated Bias filter. Updated submodule.
- Updated changelog.txt
- add conda and usegalaxy badge
- Updated submodule
- Removed updated comment
- Added fixes to integration tests due to changes in option M in Perl var2vcf_paired.pl.
- Added update for pileup amplicon references (only amplicon as somatic and simple are counted correctly) using reference result.
- Fixed type for variant in case when ref==alt (for pileup mode).
- Updated submodule.
- Fix for issue 283. Skip complex adjusting for H bases.
- Added constants.
- Updated submodule.
- Renaming.
- Added fix for #285: fill few reference fields to be available in pileup.
- Added fix for #288: factor for adjusting of qualities.
- Update HTSJDK to a more modern version and fix a typo.
- Added docs for fisher test (MLE algorithm). Added version of VarDict to expected files in integration test.
- Refactoring of printer variants for simplicity.
- Added integration test for fisher option (compare with epsilon value). Fixed scientific notation of numbers in expected VCF.
- Added option --fisher: EXPERIMENTAL FEATURE for Fisher test in Java (to exclude slow R step). Uniroot solver implemented from C version of zeroin.
- Fixes in documentation: deleted -z option from example (not useful in this case) and added explanation about BED format usage.
- Updated test case for mm10 in pileup mode and rebased.
- Added fix for issue 265: missed position when insertion/complex occurs
- Added fix for issue 272: case when end and start of cluster are equal led to zero deletion exception.
- Added IUPAC ambuguity codes fix in REF for complex/deletions .
- Added validation of reference allele.
- Added NM tag for STAR aligner: if nM is presented, it will be used.
- Fixed issue 268: added check for length of query quality sequence to skip very short strings in SV analysis.
Version 1.8.2
- Update Readme.md
- Updated integration tests to vcf 4.2
Version 1.8.1
- Updated version.
- Added validation of VCF files in integration tests. Fixed flag InDelLikely name in expected file and duplicated Bias filter. Updated submodule.
Version 1.8
- add conda and usegalaxy badge
- Updated submodule
- Removed updated comment
- Added fixes to integration tests due to changes in option M in Perl var2vcf_paired.pl.
- Added update for pileup amplicon references (only amplicon as somatic and simple are counted correctly) using reference result.
- Fixed type for variant in case when ref==alt (for pileup mode).
- Updated submodule.
- Fix for issue 283. Skip complex adjusting for H bases.
- Added constants.
- Updated submodule.
- Renaming.
- Added fix for #285: fill few reference fields to be available in pileup.
- Added fix for #288: factor for adjusting of qualities.
- Update HTSJDK to a more modern version and fix a typo.
- Added docs for fisher test (MLE algorithm). Added version of VarDict to expected files in integration test.
- Refactoring of printer variants for simplicity.
- Added integration test for fisher option (compare with epsilon value). Fixed scientific notation of numbers in expected VCF.
- Added option --fisher: EXPERIMENTAL FEATURE for Fisher test in Java (to exclude slow R step). Uniroot solver implemented from C version of zeroin.
- Fixes in documentation: deleted -z option from example (not useful in this case) and added explanation about BED format usage.
- Updated test case for mm10 in pileup mode and rebased.
- Added fix for issue 265: missed position when insertion/complex occurs
- Added fix for issue 272: case when end and start of cluster are equal led to zero deletion exception.
- Added IUPAC ambuguity codes fix in REF for complex/deletions .
- Added validation of reference allele.
- Added NM tag for STAR aligner: if nM is presented, it will be used.
- Fixed issue 268: added check for length of query quality sequence to skip very short strings in SV analysis.
Version 1.7.0
- Project updated
- Project updated
- Project updated
- Added distribution files
- Update version number
- Fixed issue with AMP in allele: hicnt and hicov for many insertions and SV were changed. Total coverage for part of the insertion changed. Added changes for chimeric reads in modify cigar part.
- Typo fixes
- Fix in description of alleles length filter
- Added explanation for bias flag
- Fixed inaccuracy in docs
- Updated changelog for 1.6.0 version
- Added commit and push for modified changelog.txt
- Added creation of release notes in release script.
- Fixed case when deletion can appear next to hard clip after modifying CIGAR.
- Added Trusty to Travis so oracleJdk8 will work.
- Fix Readme for -O option
- Fix for frequency. Test added.
- Fix README typos, grammar and markup.
- VCF updated to 4.3. specification version. MQ changed to Integer, AF field to A, BIAS contains 2 numbers.
- Also fixed one discrepancy in old part of cigar modifying for 2 insertions.
- Fixed issue 243. Cigar modify for 3 indels in case when match on reference if with a big deletion.
- Oracle JDK 12 in travis removes, added as openjdk 12
- Oracle JDK 12 in travis
- Added skipping of adaptor sequences at the end of chromosome.
- Added test case with artificial data.
- Fixed reference bases at the end of reference.
- Readme updated.
- Added options for non-monomer (--nmfreq) and monomer (--mfreq) frequency thresholds.
- Project updated
- Added VCF tests for simple and somatic modes.
Version 1.6.0
- Fixed REF allele for DEL SV: in cases when reference allele length is more than 1 base REF was not the first base in SV region, but the last one.
- Fixed genotype field: it could be displayed incorrectly (parts of genotype from different variants united) when several variants appear on one position (i.e. multiallelic). Now genotype is created for each variant separately.
- Fixed bug in the paired mode for multiallelic case: if the first variant was filtered out, the next variant skipped. Now next variants are checked also.
- Fixed bug when insertion skipped if the only insertion appears on position (and no "refvariant", very rare case in realignment).
- Fixed CIGAR modifying in three indels case and in case of possible softclips.
- Changed multiplication factor for MAPQ, QUAL and PMEAN field in the realignment of insertions, so now they don't change if the variant coverage wasn't changed by adjustment.
- Added additional sorts in algorithm parts for both Perl and Java versions in places that showed non-deterministic behavior: adjustment of MNP, realignment of insertions and deletions, the order of variants processed before output, softclips combining in consensus.
- Added loading the extended part of the reference when DEL SV with discordant pairs is calling (new DEL SV can appear after this change because now these regions also checked).
- Extended the algorithm for insertions in less than vext lenth before matched regions.
- Added CRISPR, adaptor options and fasta default paths (the same as in Perl version).
- Added SNV adjustment changes after SV calling made by Zhongwu.
- Refactoring of VarDict classes and methods structure.
Version 1.4
- Fixed error #15 and improved local realignment
Version 1.3
- Increased the size of the heap by default to 8g in start script
- Added last Zhongwu's improvements in variant amplicon
- Fixed a bug: Option 'I' had a wrong type
- Fixed issue #13: Added command-line option 'VS'