{"action":"published","release":{"url":"https://api.github.com/repos/charite/jannovar/releases/3907953","assets_url":"https://api.github.com/repos/charite/jannovar/releases/3907953/assets","upload_url":"https://uploads.github.com/repos/charite/jannovar/releases/3907953/assets{?name,label}","html_url":"https://github.com/charite/jannovar/releases/tag/v0.17","id":3907953,"tag_name":"v0.17","target_commitish":"master","name":"v0.17","draft":false,"author":{"login":"holtgrewe","id":521780,"avatar_url":"https://avatars.githubusercontent.com/u/521780?v=3","gravatar_id":"","url":"https://api.github.com/users/holtgrewe","html_url":"https://github.com/holtgrewe","followers_url":"https://api.github.com/users/holtgrewe/followers","following_url":"https://api.github.com/users/holtgrewe/following{/other_user}","gists_url":"https://api.github.com/users/holtgrewe/gists{/gist_id}","starred_url":"https://api.github.com/users/holtgrewe/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/holtgrewe/subscriptions","organizations_url":"https://api.github.com/users/holtgrewe/orgs","repos_url":"https://api.github.com/users/holtgrewe/repos","events_url":"https://api.github.com/users/holtgrewe/events{/privacy}","received_events_url":"https://api.github.com/users/holtgrewe/received_events","type":"User","site_admin":false},"prerelease":false,"created_at":"2016-08-17T14:58:58Z","published_at":"2016-08-17T15:09:51Z","assets":[],"tarball_url":"https://api.github.com/repos/charite/jannovar/tarball/v0.17","zipball_url":"https://api.github.com/repos/charite/jannovar/zipball/v0.17","body":"As with all recent releases, Jannovar is best installed through [Maven Central](https://search.maven.org).\r\nAlternatively you can directly download the compiled [jannovar-cli-0.17.jar](https://search.maven.org/remotecontent?filepath=de/charite/compbio/jannovar-cli/0.17/jannovar-cli-0.17.jar).\r\n\r\n## v0.17\r\n\r\n### jped-cli\r\n\r\n* this is gone, the functionality is now available as part of jannovar-cli\r\n\r\n### jannovar-filter\r\n\r\n* this module is done, everything here is merged into jannovar-htsjdk\r\n\r\n### jannovar-vardbs\r\n\r\n* The first version ships with support for dbSNP b147, ExAC 0.3, and the UK10K COHORT data base\r\n* Initial version of this module, the aim is precise annotation from variant databases\r\n\r\n### jannovar-cli\r\n\r\n* Updated `default_sources.ini` for latest patches of mouse and human genomes\r\n* Using one-letter amino acid code by default\r\n* Removed slf4j2 warning at program startup\r\n* Checking pedigree for compatibility with VCF file if given\r\n\r\n### jannovar-core\r\n\r\n* Adjusting API for annotating amino acid code by default\r\n* Checking pedigree for compatibility with genotypes on Mendelian inheritance checking\r\n* Refurbishing `Genotype`, `GenotypeList`, and `GenotypeListBuilder` in `de.charite.compbio.jannovar.mendel`.\r\n* Moving `ModeOfInheritance` to `de.charite.compbio.jannovar.mendel`.\r\n* Creating new package `de.charite.compbio.jannovar.mendel` with code for filtering for mendelian inheritance modes.\r\n* Renaming of `ModeOfInheritance.UNINITIALIZED` to `ModeOfInheritance.ANY`.\r\n* Fixing handling of invalid transcripts (e.g., incomplete 3' end)\r\n* Adding `altGeneIDs` mapping to `TranscriptModel`, makes data bases backwards incompatible.\r\n* Rewrite of GFF parsers for RefSeq and ENSEMBL.\r\n* Bumping HTSJDK to 2.5.0, requiring Java 8 from now on.\r\n* Removal of `AnnotationCollector`, priotization of variant effects is done after collecting all effect predictions now.\r\n* Fix for intronic variants between 5' or 3' UTRs. These variants were misclassified as `FIVE_PRIME_UTR_VARIANT` or `THREE_PRIME_UTR_VARIANT`. SequenceOntology implements new terms so that we can decide between the two UTR exon and intron variants. Now we have `FIVE_PRIME_UTR_EXON_VARIANT` or `FIVE_PRIME_UTR_EXON_INTRON_VARIANT` (the same for `THREE_PRIME_UTR_EXON_VARIANT` or `THREE_PRIME_UTR_EXON_INTRON_VARIANT`).\r\n\r\n### jannovar-cli\r\n\r\n* Adding better progress display with estimate of pending time.\r\n* Adding support for annotating values from dbSNP VCF file (currently, only b147 is supported).\r\n* Adding simple progress reporting (from verbosity level 2).\r\n* Using Java 8 stream interface for `VariantContext` processing.\r\n* Removing support for Jannovar output format, VCF offer all features and more.\r\n"}}
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