{"push_id":762413975,"size":24,"distinct_size":0,"ref":"refs/heads/master","head":"66be63bb5119ae7c88ad9dadbc83f42764ed86aa","before":"a816a4ade424f26e85d0ca8d3f20e7859a44ff37","commits":[{"sha":"be16abf8b35570b55cd94a8a70a8a700832dab51","author":{"email":"c4376ac5070e766aa94b12974a78e14463ffb77b@yahoo.com","name":"Adaminius"},"message":"initial commit for refactor","distinct":false,"url":"https://api.github.com/repos/Adaminius/psvpTools/commits/be16abf8b35570b55cd94a8a70a8a700832dab51"},{"sha":"7da1ad6eeac85231dfb5520ddd0a063a9945dcb4","author":{"email":"c4376ac5070e766aa94b12974a78e14463ffb77b@yahoo.com","name":"Adaminius"},"message":"cleanup","distinct":false,"url":"https://api.github.com/repos/Adaminius/psvpTools/commits/7da1ad6eeac85231dfb5520ddd0a063a9945dcb4"},{"sha":"59ca662ce02c13f6877eb102a6b9cd1a38334bb8","author":{"email":"c4376ac5070e766aa94b12974a78e14463ffb77b@yahoo.com","name":"Adaminius"},"message":"add initialization for class Psvp\n\nAnd other cleanup and preliminary documentation,\nalso fixed bug in psvpUtils.setupLogging","distinct":false,"url":"https://api.github.com/repos/Adaminius/psvpTools/commits/59ca662ce02c13f6877eb102a6b9cd1a38334bb8"},{"sha":"8ff568a73a95b16b0509f8821c26172bfd55ba72","author":{"email":"c4376ac5070e766aa94b12974a78e14463ffb77b@yahoo.com","name":"Adaminius"},"message":"implement psvp.Psvp.read(), add field to Site\n\nSite now has an annotations field (list[str]) for holding\nstuff not meant for the entries field. (e.g. reference\nsamples or other non-bitflag data for a site)\n\nFunctions in psvpFilter should probably also contain something\nlike an includedAnnotations list if they need to operate on\nsome of the annotations as well as the sample entries.\n\nRead seems to work ok on test data, now takes a list[int] arg\nannotationColumns and appends entries in those columns to\nsomeSite.annotations. Other entries appended to someSite.entries.\n\nSeveral constants added to mark which column read() should check\nto create Sites.","distinct":false,"url":"https://api.github.com/repos/Adaminius/psvpTools/commits/8ff568a73a95b16b0509f8821c26172bfd55ba72"},{"sha":"e5db590538ff360ec4441119b243a0dc61314e0b","author":{"email":"c4376ac5070e766aa94b12974a78e14463ffb77b@yahoo.com","name":"Adaminius"},"message":"implement write() method of class Psvp.psvp()\n\nwrite() for the psvp class now seems to be working correctly\nwhen diff'd against test data (taking into account that\npsvp.read() only preserves the first set of header lines)","distinct":false,"url":"https://api.github.com/repos/Adaminius/psvpTools/commits/e5db590538ff360ec4441119b243a0dc61314e0b"},{"sha":"f03919d2c37196b3c09e9a0693c1f121e88b3f8b","author":{"email":"c4376ac5070e766aa94b12974a78e14463ffb77b@yahoo.com","name":"Adaminius"},"message":"implement class Site, psvp.Psvp.clearMasks()\n\nSetting attributes in Site namedtuples expensive since tuples\nare immutable, so implemented a class Site in psvp.py to hold\nSite info. Chose this over a dict because usage is a bit prettier.\nAlso updated Psvp.write() to make use of class Site rather than\nthe namedtuple (now \"OldSite\").","distinct":false,"url":"https://api.github.com/repos/Adaminius/psvpTools/commits/f03919d2c37196b3c09e9a0693c1f121e88b3f8b"},{"sha":"d92b00015fb78fdc0c8b7eeb5ecd1d268ed6030e","author":{"email":"c4376ac5070e766aa94b12974a78e14463ffb77b@yahoo.com","name":"Adaminius"},"message":"implement and test clearEmptySites","distinct":false,"url":"https://api.github.com/repos/Adaminius/psvpTools/commits/d92b00015fb78fdc0c8b7eeb5ecd1d268ed6030e"},{"sha":"6c9f0610ff1af462ced68b911030cbbb339f620f","author":{"email":"c4376ac5070e766aa94b12974a78e14463ffb77b@yahoo.com","name":"Adaminius"},"message":"implement 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findType()","distinct":false,"url":"https://api.github.com/repos/Adaminius/psvpTools/commits/63e6ef0b57dab122e2cb2b6c5a08a4996601fff8"},{"sha":"c3f32985386cade8c33559c328aa77edafce856d","author":{"email":"c4376ac5070e766aa94b12974a78e14463ffb77b@yahoo.com","name":"Adaminius"},"message":"add two more filters, fix bug in psvp.Psvp\n\nAdded the filter functions psvpFilter.findAnnotated() and\npsvpFilter.findSampleSupport(), and fixed a small bug that kept\npsvp.selectiveCopy() from copying sites correctly.","distinct":false,"url":"https://api.github.com/repos/Adaminius/psvpTools/commits/c3f32985386cade8c33559c328aa77edafce856d"},{"sha":"dfc83ac43c25fa578621a05445c1e43da16a4b24","author":{"email":"c4376ac5070e766aa94b12974a78e14463ffb77b@yahoo.com","name":"Adaminius"},"message":"just making it easier to work on this at home","distinct":false,"url":"https://api.github.com/repos/Adaminius/psvpTools/commits/dfc83ac43c25fa578621a05445c1e43da16a4b24"},{"sha":"c945ff2b03a1a18c35cbaeed6d918395b6e0b20f","author":{"email":"c4376ac5070e766aa94b12974a78e14463ffb77b@yahoo.com","name":"Adaminius"},"message":"add PSVPtoVCF.py\n\nScript that converts .psvp files (which psvpTools operates with)\nto the more common VCF format.","distinct":false,"url":"https://api.github.com/repos/Adaminius/psvpTools/commits/c945ff2b03a1a18c35cbaeed6d918395b6e0b20f"},{"sha":"cbffe6d48f40a3e5d65dd6e09bfeaa48dc9405bd","author":{"email":"c4376ac5070e766aa94b12974a78e14463ffb77b@yahoo.com","name":"Adaminius"},"message":"cleanup","distinct":false,"url":"https://api.github.com/repos/Adaminius/psvpTools/commits/cbffe6d48f40a3e5d65dd6e09bfeaa48dc9405bd"},{"sha":"f24c9aea77435621bd907c38aa0e01724f151f29","author":{"email":"c4376ac5070e766aa94b12974a78e14463ffb77b@yahoo.com","name":"Adaminius"},"message":"add functionality to psvpFilter.findAnnotated()\n\nNow allows checking of specific annotations for specific contents","distinct":false,"url":"https://api.github.com/repos/Adaminius/psvpTools/commits/f24c9aea77435621bd907c38aa0e01724f151f29"},{"sha":"ac7a61a46984dd4f2ec98536531ef0c2e364007a","author":{"email":"c4376ac5070e766aa94b12974a78e14463ffb77b@yahoo.com","name":"Adaminius"},"message":"add size and overlap filters to psvpFilter","distinct":false,"url":"https://api.github.com/repos/Adaminius/psvpTools/commits/ac7a61a46984dd4f2ec98536531ef0c2e364007a"},{"sha":"935b7bfea55d8b324c85e7014e55fb279729c346","author":{"email":"c4376ac5070e766aa94b12974a78e14463ffb77b@yahoo.com","name":"Adaminius"},"message":"Add function definitions for psvpStat.py\n\nprettyPrint, pp, countSamples, and countSites are also implemented","distinct":false,"url":"https://api.github.com/repos/Adaminius/psvpTools/commits/935b7bfea55d8b324c85e7014e55fb279729c346"},{"sha":"c98a05d434053af9ac697324bccf55d4e2cf16d8","author":{"email":"c4376ac5070e766aa94b12974a78e14463ffb77b@yahoo.com","name":"Adaminius"},"message":"ignore everything in this commit\n\nNeed to work on some stuff on another machine, changes here are\nnot all working yet.","distinct":false,"url":"https://api.github.com/repos/Adaminius/psvpTools/commits/c98a05d434053af9ac697324bccf55d4e2cf16d8"},{"sha":"a7fe6e93cff4d439c76775e2b72e55ece721a307","author":{"email":"c4376ac5070e766aa94b12974a78e14463ffb77b@yahoo.com","name":"Adaminius"},"message":"add functioning psvpStat.sizeDistribution()\n\npsvpStat.sizeDistribution() is now much easier to read and seems\nto run fairly quickly.\n\nAlso made changes to psvpStat.prettyPrint() - now takes an\nOrderedDict, so distribution functions should be returning those.\nUsually should be in the form of {item/criteria : count}. This gives\na lot of flexibility in what we can give the function without having\nto make our own class for it.","distinct":false,"url":"https://api.github.com/repos/Adaminius/psvpTools/commits/a7fe6e93cff4d439c76775e2b72e55ece721a307"},{"sha":"463875dd807531375176d68bc2b11672cf230af9","author":{"email":"c4376ac5070e766aa94b12974a78e14463ffb77b@yahoo.com","name":"Adaminius"},"message":"implement psvpStat.callerDistribution()","distinct":false,"url":"https://api.github.com/repos/Adaminius/psvpTools/commits/463875dd807531375176d68bc2b11672cf230af9"}]}