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Merge branch 'releases/Release_2_11_3_Branch'
[jalview.git] / src / jalview / io / vcf / VCFLoader.java
2023-11-03 James ProcterJAL-4090 JAL-1551 spotlessApply commit | commitdiff
2023-08-10 Ben SoaresJAL-629 Change all stdout and stderr output to use... commit | commitdiff
2022-03-08 Jim ProcterJAL-3438 spotless for 2.11.2.0 commit | commitdiff
2022-02-11 Jim ProcterJAL-3949 - refactor logging from jalview.bin.Cache... commit | commitdiff
2022-02-11 Ben SoaresJAL-3949 Complete new abstracted logging framework... commit | commitdiff
2021-09-21 Ben SoaresJAL-3691 automatic insertion of Locale.ROOT to toUpperC... commit | commitdiff
2021-09-16 gmungocJAL-3761 extra check that VCF feature is fully mappable... commit | commitdiff
2020-08-10 Jim ProcterJAL-3691 toUpperCase(Locale.ROOT) for all standard... commit | commitdiff
2020-07-27 Jim ProcterJAL-3696 log the error message from the exception to... commit | commitdiff
2020-07-27 Jim ProcterJAL-3696 log the error message from the exception to... commit | commitdiff
2020-05-18 gmungocMerge branch 'Jalview-JS/develop' into develop commit | commitdiff
2020-04-21 Jim ProcterJAL-3407 add GPL license to Jalview source files commit | commitdiff
2020-03-30 gmungocMerge branch 'develop' into Jalview-JS/develop commit | commitdiff
2019-10-08 gmungocMerge branch 'develop' into Jalview-JS/develop commit | commitdiff
2019-08-22 gmungocJAL-3121 round trip GFF attributes including map-valued... commit | commitdiff
2019-07-26 gmungocMerge branch 'features/JAL-3375vcfValidation' into commit | commitdiff
2019-07-26 gmungocJAL-1793 only decode specific special characters in... commit | commitdiff
2019-07-26 gmungocJAL-3376 capture VCF POS, ID, QUAL, FILTER as feature... features/JAL-3375vcfValidation commit | commitdiff
2019-07-26 gmungocJAL-3375 format validate VCF Integer and Float fields commit | commitdiff
2019-07-25 gmungocJAL-3375 ignore '.' values for VCF data commit | commitdiff
2019-07-16 gmungocJAL-3210 Merge branch 'develop' into trialMerge commit | commitdiff
2019-07-05 gmungocJAL-1793 apply URL decoding when saving VCF attribute... commit | commitdiff
2019-06-07 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures commit | commitdiff
2019-06-07 gmungocJAL-2738 use GeneLocus extends DBRefEntry to hold chrom... commit | commitdiff
2019-06-06 gmungocMerge branch 'develop' into trialMerge commit | commitdiff
2019-05-29 gmungocJAL-2738 error logging if no ##reference found commit | commitdiff
2019-05-29 gmungocJAL-2738 accept .csi, default to GRCh37:homo_sapiens... commit | commitdiff
2019-04-29 gmungocJAL-2738 JAL-2743 update unit test to match new VCF... commit | commitdiff
2019-04-26 gmungocJAL-2738 JAL-2743 properties to map VCF header to speci... commit | commitdiff
2019-03-13 gmungocMerge branch 'develop' into trialMerge commit | commitdiff
2019-02-22 gmungocJAL-2738 don't set AF as feature score commit | commitdiff
2019-01-26 hansonrJalview.isJS() --> Platform.isJS(), DBRefEntry[] -... commit | commitdiff
2019-01-25 gmungocJAL-3187 don't compute variant features on peptide... commit | commitdiff
2017-12-04 gmungocJAL-2808 JAL-2850 update spike build to latest commit | commitdiff
2017-12-04 gmungocMerge branch 'spikes/mungo' into features/JAL-1793VCF commit | commitdiff
2017-12-04 gmungocJAL-2850 JAL-1766 option to load contig sequence refere... commit | commitdiff
2017-12-04 gmungocJAL-2845 locate reverse strand insertion as complement... commit | commitdiff
2017-12-04 gmungocJAL-2835 small refactor to only extract transcript... commit | commitdiff
2017-12-01 gmungocJAL-2835 spike updated to latest (use specific SO term... commit | commitdiff
2017-12-01 gmungocJAL-2835 refactored to extract specific consequence... commit | commitdiff
2017-11-30 gmungocJAL-2850 improved use of htsjdk api to read contig... commit | commitdiff
2017-11-27 gmungocJAL-2850 VCFLoader refactored to load VCF to contig... commit | commitdiff
2017-11-23 gmungocJAL-2808 update spike to latest (filter range, Present... commit | commitdiff
2017-11-23 gmungocJAL-2808 removed field filters; sort CSQ data by key commit | commitdiff
2017-11-15 gmungocJAL-2835 spike updated with latest commit | commitdiff
2017-11-15 gmungocJAL-2835 take all CSQ fields; catch invalid field match... commit | commitdiff
2017-11-15 gmungocJAL-2835 add filters for VCF/VEP 'fields of interest' commit | commitdiff
2017-11-13 gmungocJAL-2738 stubs for filtering VEP and VCF fields of... commit | commitdiff
2017-10-27 gmungocJAL-1793 spike branch updated to latest commit | commitdiff
2017-10-27 gmungocJAL-2792 capture feature metadata and render in Feature... commit | commitdiff
2017-10-25 gmungocJAL-2743 fall back to parsing description if chromosome... commit | commitdiff
2017-10-24 gmungocJAL-2743 slightly fancier species/assembly matching... commit | commitdiff
2017-10-20 gmungocPush 1793 latest to spike branch commit | commitdiff
2017-10-20 gmungocJAL-2755 update caller for method rename! commit | commitdiff
2017-10-11 gmungocJAL-2738 javadoc correction commit | commitdiff
2017-10-09 gmungocJAL-2738 ensure variant feature is in forward sense commit | commitdiff
2017-10-09 gmungocJAL-2738 remove commented code, unit test coverage commit | commitdiff
2017-10-05 gmungocJAL-2738 update spikes/mungo commit | commitdiff
2017-10-05 gmungocJAL-2738 warn (in console) when non chromosomal coordin... commit | commitdiff
2017-10-04 gmungocJAL-2738 fix bug of premature exit from adding attributes commit | commitdiff
2017-10-04 gmungocJAL-2738 match consequence "Allele" to VCF allele;... commit | commitdiff
2017-10-03 gmungocJAL-2738 copy to spikes/mungo commit | commitdiff
2017-10-03 gmungocJAL-2738 code formatting commit | commitdiff
2017-10-02 gmungocJAL-2738 code tidy up, null checks &c commit | commitdiff
2017-10-02 gmungocJAL-2738 filter VEP consequence data to that for curren... commit | commitdiff
2017-09-29 gmungocJAL-2738 one sequence feature per (SNP) VCF allele commit | commitdiff
2017-09-28 gmungocJAL-2738 separate thread to load VCF; update FeatureSet... commit | commitdiff
2017-09-28 gmungocJAL-1796 GeneLociI as distinguished DBRefEntry commit | commitdiff
2017-09-26 gmungocJAL-2738 transfer VCF variant features to CDS sequences commit | commitdiff
2017-09-26 gmungocJAL-2738 unit test for reverse strand gene commit | commitdiff
2017-09-25 gmungocJAL-2738 use complement base for a VCF variant on rever... commit | commitdiff
2017-09-25 gmungocJAL-2738 one constant in codebase for "alleles" attribu... commit | commitdiff
2017-09-25 gmungocJAL-2738 extract SNP variants from SNP or MIXED variant... commit | commitdiff
2017-09-22 gmungocJAL-2738 extract utility method to MappingUtils commit | commitdiff
2017-09-22 gmungocJAL-2738 correct handling of reverse strand genes commit | commitdiff
2017-09-22 gmungocJAL-2738 lookup GRCh38/37 gene mapping commit | commitdiff
2017-09-21 gmungocJAL-2738 compute VCF on peptide, extract AF (allele... commit | commitdiff
2017-09-21 gmungocJAL-2738 PoC of Load VCF file on to gene sequence commit | commitdiff