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JAL-2305 comments re testFindXrefSequences_withFetch is failing - looks like test...
[jalview.git] / src / jalview / io / vcf /
2021-09-21 Ben SoaresJAL-3691 automatic insertion of Locale.ROOT to toUpperC... tree | commitdiff
2021-09-16 gmungocJAL-3761 extra check that VCF feature is fully mappable... tree | commitdiff
2020-07-27 Jim ProcterJAL-3696 log the error message from the exception to... tree | commitdiff
2020-05-18 gmungocMerge branch 'Jalview-JS/develop' into develop tree | commitdiff
2020-04-21 Jim ProcterJAL-3407 add GPL license to Jalview source files tree | commitdiff
2020-03-30 gmungocMerge branch 'develop' into Jalview-JS/develop tree | commitdiff
2019-10-08 gmungocMerge branch 'develop' into Jalview-JS/develop tree | commitdiff
2019-08-22 gmungocJAL-3121 round trip GFF attributes including map-valued... tree | commitdiff
2019-07-26 gmungocMerge branch 'features/JAL-3375vcfValidation' into tree | commitdiff
2019-07-26 gmungocJAL-1793 only decode specific special characters in... tree | commitdiff
2019-07-26 gmungocJAL-3376 capture VCF POS, ID, QUAL, FILTER as feature... features/JAL-3375vcfValidation tree | commitdiff
2019-07-26 gmungocJAL-3375 format validate VCF Integer and Float fields tree | commitdiff
2019-07-25 gmungocJAL-3375 ignore '.' values for VCF data tree | commitdiff
2019-07-16 gmungocJAL-3210 Merge branch 'develop' into trialMerge tree | commitdiff
2019-07-05 gmungocJAL-1793 apply URL decoding when saving VCF attribute... tree | commitdiff
2019-06-07 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures tree | commitdiff
2019-06-07 gmungocJAL-2738 use GeneLocus extends DBRefEntry to hold chrom... tree | commitdiff
2019-06-06 gmungocMerge branch 'develop' into trialMerge tree | commitdiff
2019-05-29 gmungocJAL-2738 error logging if no ##reference found tree | commitdiff
2019-05-29 gmungocJAL-2738 accept .csi, default to GRCh37:homo_sapiens... tree | commitdiff
2019-04-29 gmungocJAL-2738 JAL-2743 update unit test to match new VCF... tree | commitdiff
2019-04-26 gmungocJAL-2738 JAL-2743 properties to map VCF header to speci... tree | commitdiff
2019-03-13 gmungocMerge branch 'develop' into trialMerge tree | commitdiff
2019-02-22 gmungocJAL-2738 don't set AF as feature score tree | commitdiff
2019-01-26 hansonrJalview.isJS() --> Platform.isJS(), DBRefEntry[] -... tree | commitdiff
2019-01-25 gmungocJAL-3187 don't compute variant features on peptide... tree | commitdiff
2017-12-04 gmungocJAL-2808 JAL-2850 update spike build to latest tree | commitdiff
2017-12-04 gmungocMerge branch 'spikes/mungo' into features/JAL-1793VCF tree | commitdiff
2017-12-04 gmungocJAL-2850 JAL-1766 option to load contig sequence refere... tree | commitdiff
2017-12-04 gmungocJAL-2845 locate reverse strand insertion as complement... tree | commitdiff
2017-12-04 gmungocJAL-2835 small refactor to only extract transcript... tree | commitdiff
2017-12-01 gmungocJAL-2835 spike updated to latest (use specific SO term... tree | commitdiff
2017-12-01 gmungocJAL-2835 refactored to extract specific consequence... tree | commitdiff
2017-11-30 gmungocJAL-2850 improved use of htsjdk api to read contig... tree | commitdiff
2017-11-27 gmungocJAL-2850 VCFLoader refactored to load VCF to contig... tree | commitdiff
2017-11-23 gmungocJAL-2808 update spike to latest (filter range, Present... tree | commitdiff
2017-11-23 gmungocJAL-2808 removed field filters; sort CSQ data by key tree | commitdiff
2017-11-15 gmungocJAL-2835 spike updated with latest tree | commitdiff
2017-11-15 gmungocJAL-2835 take all CSQ fields; catch invalid field match... tree | commitdiff
2017-11-15 gmungocJAL-2835 add filters for VCF/VEP 'fields of interest' tree | commitdiff
2017-11-13 gmungocJAL-2738 stubs for filtering VEP and VCF fields of... tree | commitdiff
2017-10-27 gmungocJAL-1793 spike branch updated to latest tree | commitdiff
2017-10-27 gmungocJAL-2792 capture feature metadata and render in Feature... tree | commitdiff
2017-10-25 gmungocJAL-2743 fall back to parsing description if chromosome... tree | commitdiff
2017-10-24 gmungocJAL-2743 slightly fancier species/assembly matching... tree | commitdiff
2017-10-20 gmungocPush 1793 latest to spike branch tree | commitdiff
2017-10-20 gmungocJAL-2755 update caller for method rename! tree | commitdiff
2017-10-11 gmungocJAL-2738 javadoc correction tree | commitdiff
2017-10-09 gmungocJAL-2738 ensure variant feature is in forward sense tree | commitdiff
2017-10-09 gmungocJAL-2738 remove commented code, unit test coverage tree | commitdiff
2017-10-05 gmungocJAL-2738 update spikes/mungo tree | commitdiff
2017-10-05 gmungocJAL-2738 warn (in console) when non chromosomal coordin... tree | commitdiff
2017-10-04 gmungocJAL-2738 fix bug of premature exit from adding attributes tree | commitdiff
2017-10-04 gmungocJAL-2738 match consequence "Allele" to VCF allele;... tree | commitdiff
2017-10-03 gmungocJAL-2738 copy to spikes/mungo tree | commitdiff
2017-10-03 gmungocJAL-2738 code formatting tree | commitdiff
2017-10-02 gmungocJAL-2738 code tidy up, null checks &c tree | commitdiff
2017-10-02 gmungocJAL-2738 filter VEP consequence data to that for curren... tree | commitdiff
2017-09-29 gmungocJAL-2738 one sequence feature per (SNP) VCF allele tree | commitdiff
2017-09-28 gmungocJAL-2738 separate thread to load VCF; update FeatureSet... tree | commitdiff
2017-09-28 gmungocJAL-1796 GeneLociI as distinguished DBRefEntry tree | commitdiff
2017-09-26 gmungocJAL-2738 transfer VCF variant features to CDS sequences tree | commitdiff
2017-09-26 gmungocJAL-2738 unit test for reverse strand gene tree | commitdiff
2017-09-25 gmungocJAL-2738 use complement base for a VCF variant on rever... tree | commitdiff
2017-09-25 gmungocJAL-2738 one constant in codebase for "alleles" attribu... tree | commitdiff
2017-09-25 gmungocJAL-2738 extract SNP variants from SNP or MIXED variant... tree | commitdiff
2017-09-22 gmungocJAL-2738 extract utility method to MappingUtils tree | commitdiff
2017-09-22 gmungocJAL-2738 correct handling of reverse strand genes tree | commitdiff
2017-09-22 gmungocJAL-2738 lookup GRCh38/37 gene mapping tree | commitdiff
2017-09-21 gmungocJAL-2738 compute VCF on peptide, extract AF (allele... tree | commitdiff
2017-09-21 gmungocJAL-2738 PoC of Load VCF file on to gene sequence tree | commitdiff