GitHub PushEvent at 2014-08-28 07:58:38
Repository: piper
Actor: johandahlberg
Payload: {"shas":[["4ae088e17bb73794a3235593da095dbd33f08d23","c639c92385b071f79005270c95e1d69c87dfa9d7@medsci.uu.se","Lowering compression level of GATK tools...\n\n... should give some performance benefits, while losing very little in\nin terms of file size.","Johan Dahlberg",false],["3f21fbb4fcea7853a48e64c2d2011175b044df5d","c639c92385b071f79005270c95e1d69c87dfa9d7@medsci.uu.se","Fixing DNABestPracticeVariantCalling for non-human\n\nThis means some perhaps subtle changes. I moved to notHuman option into\nthe GATKConfig class as this is now used both in variant calling and\ndata processing. This idea is that now the FileAndProgramResourceConfig\ntrait will not load the default (human) resource files, and thus defer\nthem to what's been set on the command line. This should mean that the\nhuman files are not loaded when it goes into the dataprocessing and thus\nare not used.","Johan Dahlberg",false],["137ec37be124c7a19849c9898f33b8380b893691","c639c92385b071f79005270c95e1d69c87dfa9d7@medsci.uu.se","The last value is the flowcell id.\n\nCloses issue #26.","Johan Dahlberg",false],["074bf152cedd21d694c450e71d2d10675cb493ff","c639c92385b071f79005270c95e1d69c87dfa9d7@medsci.uu.se","Moving old Setup xml stuff into legacy namespace\n\nMaking room for the new stuff.","Johan Dahlberg",false],["9c73907b47374ed0107cbfc5ab96f07d0ad192e7","c639c92385b071f79005270c95e1d69c87dfa9d7@medsci.uu.se","WIP Fixing setupFileCreator with new format","Johan Dahlberg",false],["553a7a173cce4e3fc323c9314da19ade6adfebb8","c639c92385b071f79005270c95e1d69c87dfa9d7@medsci.uu.se","Some more comments and extra help at exception.","Johan Dahlberg",false],["41305d560a349a02dc559d0aa7b77d53fcb313ac","c639c92385b071f79005270c95e1d69c87dfa9d7@medsci.uu.se","New SetupXMLReader implemented","Johan Dahlberg",false],["5cc31177fb67f4ef858dd78205b1e6ff226291b7","c639c92385b071f79005270c95e1d69c87dfa9d7@medsci.uu.se","Adding tests for the new setup reader\n\nI just copied the tests for the legacy reader and made sure that if it\ncontained the same informtation, the reader would return the same info,\nand that seems to be working.","Johan Dahlberg",false],["62d06d94ca85fdca516415bd384125c6fe5ee547","c639c92385b071f79005270c95e1d69c87dfa9d7@medsci.uu.se","Add test for reader switching","Johan Dahlberg",false],["2fc617642d4369143ab3ddcc969bc1e10f8201fe","c639c92385b071f79005270c95e1d69c87dfa9d7@medsci.uu.se","Switch SetupXMLReader by looking for <runfolder>\n\nIf this tag is present it will be assumed that this is a file on the\nlegacy format.","Johan Dahlberg",false],["6d7f2fd165c96a026e33fe2c8554233de70959fa","c639c92385b071f79005270c95e1d69c87dfa9d7@medsci.uu.se","Update the README with new input format","Johan Dahlberg",false],["90db2950ffdd49fc93a8a84ba5277bb54208360a","c639c92385b071f79005270c95e1d69c87dfa9d7@medsci.uu.se","WIP Setting up report generator","Johan Dahlberg",false],["0a415a6d437f0685357614f9a311ae2c228d30b8","c639c92385b071f79005270c95e1d69c87dfa9d7@medsci.uu.se","WIP Creating report files\n\nCan now get piper, GATK and program version. Still need to get resource\nversions.","Johan Dahlberg",false],["2a8a0d1ffd2b80c3549740a2d7b4e381497bf748","c639c92385b071f79005270c95e1d69c87dfa9d7@medsci.uu.se","WIP: report function for DNA_BPVC is done\n\nStill need to add it to the qscript and test it.","Johan Dahlberg",false],["33aae34e036abdbb6ae659f9c65d8d7247bb457b","c639c92385b071f79005270c95e1d69c87dfa9d7@medsci.uu.se","Added the report creation to DNA_BPVC","Johan Dahlberg",false],["135bc7518ef5e30c5baf12608b652c18fa2379af","c639c92385b071f79005270c95e1d69c87dfa9d7@medsci.uu.se","Even empty maps need to return a none-value","Johan Dahlberg",false],["1922a4788216d3bbce141a477093aa63d950ef50","c639c92385b071f79005270c95e1d69c87dfa9d7@medsci.uu.se","Added missing else clause...\n\nWhich caused there to always be a empty return","Johan Dahlberg",false],["8de18be73e300afa18217a2f030cd3db30740553","c639c92385b071f79005270c95e1d69c87dfa9d7@medsci.uu.se","Adding version numbers to uppmax_global_config","Johan Dahlberg",false],["60c3956c9d56d757e9781c30231bf0e79708811a","c639c92385b071f79005270c95e1d69c87dfa9d7@medsci.uu.se","Make sure to always send a map with default value","Johan Dahlberg",false],["2d69cf87ba51654e7dee3823a2645770f56c2a0e","c639c92385b071f79005270c95e1d69c87dfa9d7@medsci.uu.se","Transcripts and Annotations are the same thing...\n\n... so no need to keep both as far as I can see.","Johan Dahlberg",false]],"size":23,"ref":"refs/heads/master","head":"773c2061dad21480df053c7fc914f6f44ef734a3"}