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JAL-4101 Updated DEFAULT_RFAM_BASEURL
[jalview.git]
/
src
/
jalview
/
io
/
vcf
/
VCFLoader.java
2022-03-08
Jim Procter
JAL-3438 spotless for 2.11.2.0
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commitdiff
2022-02-11
Jim Procter
JAL-3949 - refactor logging from jalview.bin.Cache...
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2022-02-11
Ben Soares
JAL-3949 Complete new abstracted logging framework...
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diff to current
2021-09-21
Ben Soares
JAL-3691 automatic insertion of Locale.ROOT to toUpperC...
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diff to current
2021-09-16
gmungoc
JAL-3761 extra check that VCF feature is fully mappable...
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diff to current
2020-08-10
Jim Procter
JAL-3691 toUpperCase(Locale.ROOT) for all standard...
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2020-07-27
Jim Procter
JAL-3696 log the error message from the exception to...
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2020-07-27
Jim Procter
JAL-3696 log the error message from the exception to...
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commitdiff
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2020-05-18
gmungoc
Merge branch 'Jalview-JS/develop' into develop
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2020-04-21
Jim Procter
JAL-3407 add GPL license to Jalview source files
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2020-03-30
gmungoc
Merge branch 'develop' into Jalview-JS/develop
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2019-10-08
gmungoc
Merge branch 'develop' into Jalview-JS/develop
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2019-08-22
gmungoc
JAL-3121 round trip GFF attributes including map-valued...
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2019-07-26
gmungoc
Merge branch 'features/JAL-3375vcfValidation' into
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2019-07-26
gmungoc
JAL-1793 only decode specific special characters in...
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2019-07-26
gmungoc
JAL-3376 capture VCF POS, ID, QUAL, FILTER as feature...
features/JAL-3375vcfValidation
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2019-07-26
gmungoc
JAL-3375 format validate VCF Integer and Float fields
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2019-07-25
gmungoc
JAL-3375 ignore '.' values for VCF data
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2019-07-16
gmungoc
JAL-3210 Merge branch 'develop' into trialMerge
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2019-07-05
gmungoc
JAL-1793 apply URL decoding when saving VCF attribute...
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2019-06-07
gmungoc
Merge branch 'develop' into feature/JAL-3187linkedFeatures
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2019-06-07
gmungoc
JAL-2738 use GeneLocus extends DBRefEntry to hold chrom...
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2019-06-06
gmungoc
Merge branch 'develop' into trialMerge
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2019-05-29
gmungoc
JAL-2738 error logging if no ##reference found
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2019-05-29
gmungoc
JAL-2738 accept .csi, default to GRCh37:homo_sapiens...
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2019-04-29
gmungoc
JAL-2738 JAL-2743 update unit test to match new VCF...
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2019-04-26
gmungoc
JAL-2738 JAL-2743 properties to map VCF header to speci...
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2019-03-13
gmungoc
Merge branch 'develop' into trialMerge
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2019-02-22
gmungoc
JAL-2738 don't set AF as feature score
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2019-01-26
hansonr
Jalview.isJS() --> Platform.isJS(), DBRefEntry[] -...
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2019-01-25
gmungoc
JAL-3187 don't compute variant features on peptide...
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2017-12-04
gmungoc
JAL-2808 JAL-2850 update spike build to latest
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2017-12-04
gmungoc
Merge branch 'spikes/mungo' into features/JAL-1793VCF
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2017-12-04
gmungoc
JAL-2850 JAL-1766 option to load contig sequence refere...
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2017-12-04
gmungoc
JAL-2845 locate reverse strand insertion as complement...
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2017-12-04
gmungoc
JAL-2835 small refactor to only extract transcript...
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2017-12-01
gmungoc
JAL-2835 spike updated to latest (use specific SO term...
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2017-12-01
gmungoc
JAL-2835 refactored to extract specific consequence...
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2017-11-30
gmungoc
JAL-2850 improved use of htsjdk api to read contig...
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2017-11-27
gmungoc
JAL-2850 VCFLoader refactored to load VCF to contig...
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2017-11-23
gmungoc
JAL-2808 update spike to latest (filter range, Present...
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2017-11-23
gmungoc
JAL-2808 removed field filters; sort CSQ data by key
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2017-11-15
gmungoc
JAL-2835 spike updated with latest
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2017-11-15
gmungoc
JAL-2835 take all CSQ fields; catch invalid field match...
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2017-11-15
gmungoc
JAL-2835 add filters for VCF/VEP 'fields of interest'
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2017-11-13
gmungoc
JAL-2738 stubs for filtering VEP and VCF fields of...
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2017-10-27
gmungoc
JAL-1793 spike branch updated to latest
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2017-10-27
gmungoc
JAL-2792 capture feature metadata and render in Feature...
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2017-10-25
gmungoc
JAL-2743 fall back to parsing description if chromosome...
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2017-10-24
gmungoc
JAL-2743 slightly fancier species/assembly matching...
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2017-10-20
gmungoc
Push 1793 latest to spike branch
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2017-10-20
gmungoc
JAL-2755 update caller for method rename!
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2017-10-11
gmungoc
JAL-2738 javadoc correction
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2017-10-09
gmungoc
JAL-2738 ensure variant feature is in forward sense
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2017-10-09
gmungoc
JAL-2738 remove commented code, unit test coverage
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2017-10-05
gmungoc
JAL-2738 update spikes/mungo
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2017-10-05
gmungoc
JAL-2738 warn (in console) when non chromosomal coordin...
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2017-10-04
gmungoc
JAL-2738 fix bug of premature exit from adding attributes
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2017-10-04
gmungoc
JAL-2738 match consequence "Allele" to VCF allele;...
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2017-10-03
gmungoc
JAL-2738 copy to spikes/mungo
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commitdiff
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2017-10-03
gmungoc
JAL-2738 code formatting
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2017-10-02
gmungoc
JAL-2738 code tidy up, null checks &c
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2017-10-02
gmungoc
JAL-2738 filter VEP consequence data to that for curren...
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2017-09-29
gmungoc
JAL-2738 one sequence feature per (SNP) VCF allele
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2017-09-28
gmungoc
JAL-2738 separate thread to load VCF; update FeatureSet...
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2017-09-28
gmungoc
JAL-1796 GeneLociI as distinguished DBRefEntry
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2017-09-26
gmungoc
JAL-2738 transfer VCF variant features to CDS sequences
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2017-09-26
gmungoc
JAL-2738 unit test for reverse strand gene
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2017-09-25
gmungoc
JAL-2738 use complement base for a VCF variant on rever...
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2017-09-25
gmungoc
JAL-2738 one constant in codebase for "alleles" attribu...
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diff to current
2017-09-25
gmungoc
JAL-2738 extract SNP variants from SNP or MIXED variant...
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2017-09-22
gmungoc
JAL-2738 extract utility method to MappingUtils
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diff to current
2017-09-22
gmungoc
JAL-2738 correct handling of reverse strand genes
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commitdiff
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diff to current
2017-09-22
gmungoc
JAL-2738 lookup GRCh38/37 gene mapping
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diff to current
2017-09-21
gmungoc
JAL-2738 compute VCF on peptide, extract AF (allele...
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diff to current
2017-09-21
gmungoc
JAL-2738 PoC of Load VCF file on to gene sequence
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diff to current