{"push_id":635408213,"size":55,"distinct_size":5,"ref":"refs/heads/add_rna_schema","head":"74bd535432150b51af63355eaa1fbda3e87ef59d","before":"1d18151b19e7585272900e548ed6916f84dffacd","commits":[{"sha":"91e657549bd8e9ab66021435323a0bae539c95c3","author":{"email":"0e779b910d3a07c20c5112429ccd7eaa900865ed@soe.ucsc.edu","name":"adamnovak"},"message":"Document topic branches\n\nSince we made the graph branch, and since I just moved the branch pointer unilaterally, I figured I ought to legitimize such things. This commit updates the contributing document to describe how I think topic branches like this ought to be handled.","distinct":false,"url":"https://api.github.com/repos/saupchurch/schemas/commits/91e657549bd8e9ab66021435323a0bae539c95c3"},{"sha":"4c272aa3db9d952beeac4627e038f6dc2e2ae45c","author":{"email":"0e779b910d3a07c20c5112429ccd7eaa900865ed@soe.ucsc.edu","name":"Adam Novak"},"message":"Upping pom.xml version\n\nI'm setting the version in `pom.xml` to 0.6.0-SNAPSHOT, meaning we're currently in the process of developing version 0.6.0 of the schemas. We definitely have to have a version greater than 0.5.1, since that's our latest release, and since then we've made a number of potentially breaking changes, like stripping the \"GA\" prefixes off of everything, so I figured we would want to start with the 0.6 series.\n\nIn the future, when we do a release we ought to set this to exactly the version we release (so the tagged v0.6.0 release should have 0.6.0 here). The tagged v0.5.1 reports itself as \"0.1.0-SNAPSHOT\", which is a bit of a problem if anyone wants to depend on our compiled schema JARs.\n\nCloses #197.","distinct":false,"url":"https://api.github.com/repos/saupchurch/schemas/commits/4c272aa3db9d952beeac4627e038f6dc2e2ae45c"},{"sha":"cada42f78ea2fe0a86b51c793e40bbef3eec0b30","author":{"email":"0e779b910d3a07c20c5112429ccd7eaa900865ed@soe.ucsc.edu","name":"adamnovak"},"message":"Require review of all (and only) actual commits\n\nIf you want to fast-forward a branch up to master you can, but if there is actual merging involved you need to pull request it for review.","distinct":false,"url":"https://api.github.com/repos/saupchurch/schemas/commits/cada42f78ea2fe0a86b51c793e40bbef3eec0b30"},{"sha":"b9c7510965a021de63a4cb1cd9c61aea129f1499","author":{"email":"0e779b910d3a07c20c5112429ccd7eaa900865ed@soe.ucsc.edu","name":"adamnovak"},"message":"Making Jerome's changes\n\nHopefully slightly clearer to read now. @jeromekelleher?","distinct":false,"url":"https://api.github.com/repos/saupchurch/schemas/commits/b9c7510965a021de63a4cb1cd9c61aea129f1499"},{"sha":"1711d81d9a4242a0020fdf0cb85b1700727beda7","author":{"email":"7841830342f748a54814a395669113bed0a8f742@cs.berkeley.edu","name":"Matt Massie"},"message":"Move models and RPC methods out of root package\n\nThis updates the namespace to place the models into the\norg.ga4gh.models package and RPC methods into the\norg.ga4gh.rpc package. Previously, all objects were on\nthe root package org.ga4gh.","distinct":false,"url":"https://api.github.com/repos/saupchurch/schemas/commits/1711d81d9a4242a0020fdf0cb85b1700727beda7"},{"sha":"940fa35b0216c28177a4b5c209fefd3b722e933e","author":{"email":"0e779b910d3a07c20c5112429ccd7eaa900865ed@soe.ucsc.edu","name":"Adam Novak"},"message":"Fixing whitespace to be up to spec.","distinct":false,"url":"https://api.github.com/repos/saupchurch/schemas/commits/940fa35b0216c28177a4b5c209fefd3b722e933e"},{"sha":"46065e0983d80659805b37998bdc15c61bf0d608","author":{"email":"9c9a8f9ef7ef451b162cf8d00aed16e3dfc34bc3@users.noreply.github.com","name":"Angel Pizarro"},"message":"Merge pull request #209 from massie/namespace\n\nMove models and RPC methods out of root package","distinct":false,"url":"https://api.github.com/repos/saupchurch/schemas/commits/46065e0983d80659805b37998bdc15c61bf0d608"},{"sha":"2cbb1dca3b33ef6f9929111bc1976be5fed89a02","author":{"email":"9c9a8f9ef7ef451b162cf8d00aed16e3dfc34bc3@gmail.com","name":"Angel Pizarro"},"message":"Merged conflicts from #209 and #205.","distinct":false,"url":"https://api.github.com/repos/saupchurch/schemas/commits/2cbb1dca3b33ef6f9929111bc1976be5fed89a02"},{"sha":"1dfcdeab10ca618333b05fc45f19d63c129b9c0f","author":{"email":"9c9a8f9ef7ef451b162cf8d00aed16e3dfc34bc3@gmail.com","name":"Angel Pizarro"},"message":"Merge branch 'adamnovak-whitespace'.\n\nThis was a merge of conflicts between PR #209 and #205. Whitespace issues\nnow integrated with the namespacing of methods and models.","distinct":false,"url":"https://api.github.com/repos/saupchurch/schemas/commits/1dfcdeab10ca618333b05fc45f19d63c129b9c0f"},{"sha":"256c715dbbfdf343ed24cba95568925987880492","author":{"email":"9c9a8f9ef7ef451b162cf8d00aed16e3dfc34bc3@users.noreply.github.com","name":"Angel Pizarro"},"message":"Merge pull request #200 from adamnovak/version\n\nUpping pom.xml version","distinct":false,"url":"https://api.github.com/repos/saupchurch/schemas/commits/256c715dbbfdf343ed24cba95568925987880492"},{"sha":"c6c7d7f611b1057751679c97d9ae4551a6e43467","author":{"email":"9c9a8f9ef7ef451b162cf8d00aed16e3dfc34bc3@users.noreply.github.com","name":"Angel Pizarro"},"message":"Merge pull request #199 from adamnovak/styleGuide\n\nDocument topic branches","distinct":false,"url":"https://api.github.com/repos/saupchurch/schemas/commits/c6c7d7f611b1057751679c97d9ae4551a6e43467"},{"sha":"a45792fe63548c562b90da3057aa005cb75086ac","author":{"email":"f30dc31842608073ca9a54ef65e56d919c0c17bc@gmail.com","name":"Michael Baudis"},"message":"Update and rename src/main/resources/avro/wip/metadata.avdl to src/main/resources/avro/metadata.avdl","distinct":false,"url":"https://api.github.com/repos/saupchurch/schemas/commits/a45792fe63548c562b90da3057aa005cb75086ac"},{"sha":"f8e88bfe4bc8a53ac00f94ca7423bfd1f91db106","author":{"email":"f30dc31842608073ca9a54ef65e56d919c0c17bc@gmail.com","name":"Michael Baudis"},"message":"Update and rename src/main/resources/avro/wip/metadatamethods.avdl to src/main/resources/avro/metadatamethods.avdl","distinct":false,"url":"https://api.github.com/repos/saupchurch/schemas/commits/f8e88bfe4bc8a53ac00f94ca7423bfd1f91db106"},{"sha":"ab205456cac0e299a2125da4aa57b28582038aee","author":{"email":"98251f16f669927a8dcb0567c15a695a3a4b76bb@soe.ucsc.edu","name":"Mark Diekhans"},"message":"Merge pull request #213 from mbaudis/master\n\nMoving metadata out of WIP","distinct":false,"url":"https://api.github.com/repos/saupchurch/schemas/commits/ab205456cac0e299a2125da4aa57b28582038aee"},{"sha":"1d0225c2b9c16cf7ca7fbcbc431b84abdbb51a68","author":{"email":"98251f16f669927a8dcb0567c15a695a3a4b76bb@soe.ucsc.edu","name":"Mark Diekhans"},"message":"Represent stand as enum/symbolic value rather than a boolean.  This\nis both more natural and supports unstranded positions.","distinct":false,"url":"https://api.github.com/repos/saupchurch/schemas/commits/1d0225c2b9c16cf7ca7fbcbc431b84abdbb51a68"},{"sha":"49616fedf2fc35d514dd06e52079c8133fdb1c6e","author":{"email":"98251f16f669927a8dcb0567c15a695a3a4b76bb@soe.ucsc.edu","name":"Mark Diekhans"},"message":"Convert representation of sex to use OntologyTerm rather than have\na special case enum that is different than all other metadata.","distinct":false,"url":"https://api.github.com/repos/saupchurch/schemas/commits/49616fedf2fc35d514dd06e52079c8133fdb1c6e"},{"sha":"b010f064148f6bdd21bf7aefcd1622de65adbd09","author":{"email":"1b7fbefd792d7a9793d7aac527d8c759c32763c6@alumni.stanford.edu","name":"Frank Austin Nothaft"},"message":"Merge pull request #237 from diekhans/symbolic-strand\n\nRepresent stand as enum/symbolic value rather than a boolean.","distinct":false,"url":"https://api.github.com/repos/saupchurch/schemas/commits/b010f064148f6bdd21bf7aefcd1622de65adbd09"},{"sha":"a88e0395e998cf5c8b72a276a474cf8751e55464","author":{"email":"1b6e9755e4d46d522345d16f3df0b5fada15bc41@gmail.com","name":"Steven G. Hershman"},"message":"updated beacon.avro to 0.2 spec","distinct":false,"url":"https://api.github.com/repos/saupchurch/schemas/commits/a88e0395e998cf5c8b72a276a474cf8751e55464"},{"sha":"e6d6074d4b95dab7c0ba9a357a6adba338ed1daf","author":{"email":"68a658b44bbaefab3ef5cd231967195fc0ff9d69@well.ox.ac.uk","name":"Jerome Kelleher"},"message":"Merge pull request #235 from hershman/master\n\nUpdated beacon to 0.2","distinct":false,"url":"https://api.github.com/repos/saupchurch/schemas/commits/e6d6074d4b95dab7c0ba9a357a6adba338ed1daf"},{"sha":"346bfc3848864f19352f9e03a7cbac4519378ab4","author":{"email":"0e779b910d3a07c20c5112429ccd7eaa900865ed@soe.ucsc.edu","name":"Adam Novak"},"message":"Bringing graph support to Common, Reads, and References\n\nThere is now a `Path` and `Segment` in a graph namespace in common.avdl, and a\n`GraphAlignment` in the graph namespace in reads.avdl. We also have a\n`/graph/sequence/{id}` endpoint to get sequence bases in a generic way, and a\ncouple more options to search by.\n\nAdding support for monoallelic calls.\n\nThis adds an `Allele` type, and allows for `Call`s to be associated with\n`Allele`s, or with `Allele`s and `Variant`s.\n\n`Allele`s can be used to represent the ref and alt alleles of `Varaint`s.\n\nWe also provide for associating new sequences with `VariantSet`s.\n\nRemoving graph namespace and URL prefix\n\nRevising comments and field names\n\nUnifying checksums\n\nRevising variants comments\n\nCode reviewed by Prof. Haussler\n\nChanging comments to be more descriptive and mathematically tight.\n\nAlso catching a few typos.\n\nFixing oversights in new API calls\n\nAdding in primer on sequence graphs\n\nRevising David's sequence graph intro\n\nExplaining sequence search better\n\nSequences are searched over, and results are returned as segments describing\nsequences.\n\nAlso removing references to an out-of-date object name.\n\nRemoving update timestamp from Allele\n\nClarifying sequences, segments, and references\n\nFixing up whitespace\n\nIntroducing \"graph\" and \"classic\" modes.\n\nA server can support \"graph\" mode, \"classic\" mode, or both.\n\nIf it supports \"classic\" mode, it will make sure to fill in all of\nthe fields that non-graph clients require, and not use incompatible\ngraph extensions like `GraphAlignment`.\n\nIf it supports \"graph\" mode, it will make sure to fill in all of the new\ngraph fields, like `Reference.segment` and `Variant.alleles`. Additionally,\nif it also does not support \"classic\" mode, it will not use older, less\ngeneral things like `LinearAlignment` and single string phase sets.\n\nMaking David's documentation changes\n\nAlso adding more pictures and hammering on the parent/child distinction.\n\nMaking startJoin and endJoin default to null\n\nClarifying the order of segments in a path\n\nFixing example typos\n\nSplitting out `AlleleCall`.\n\nThere is now an `AlleleCall` to take care of calling copy numbers of `Alleles`,\nwhile the normal `Call` goes back to just handling genotypes. I also stripped\nsome of the bachwards-compatibility warts off of `AlleleCall`, since it has no\nlegacy fields to keep.\n\nBoth kinds of calls are constrained to be consistent with each other; you\ncan't call a genotype of [1, 1], and have a copy number of 0 for that allele\nin that variant.\n\nIf you support \"graph\" mode, you have to serve `AlleleCall`s for every\n`Variant` you have `Call`s on, and visa versa if you support \"classic\" mode.\n\nMore descriptive name for new method\n\nFixing case where it would be impossible to get allele sequence.\n\nSince a `Position` can be specified by `Reference` name, there is no\nefficient way to search for a `Reference` by name, and the only way to get\nsequence bases (in the old and proposed APIs) is by ID, we need to be able\nto make sure that all `Position`s include IDs in the graph mode, so we can\nactually get the sequence.\n\nFixing doc comment typos\n\nClarifying computation of `Reference.md5checksum`.\n\nI now give an explicit procedure for how you are supposed to compute the\n`md5checksum` of a `Reference`. It no longer makes reference to the idea of a\nchecksum for a `Position`, since that doesn't actually exist.\n\nIt should be much clearer now what is to be hashed, which is important because\neveryone needs to do the same thing to get the same hashes.","distinct":false,"url":"https://api.github.com/repos/saupchurch/schemas/commits/346bfc3848864f19352f9e03a7cbac4519378ab4"}]}