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changelog.txt
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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'