{"action":"created","comment":{"url":"https://api.github.com/repos/icgc-dcc/dcc-portal/pulls/comments/57570148","id":57570148,"diff_hunk":"@@ -0,0 +1,610 @@\n+/*\n+ * Copyright (c) 2016 The Ontario Institute for Cancer Research. All rights reserved.\n+ *\n+ * This program and the accompanying materials are made available under the terms of the GNU Public License v3.0.\n+ * You should have received a copy of the GNU General Public License along with\n+ * this program. If not, see <http://www.gnu.org/licenses/>.\n+ *\n+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\" AND ANY\n+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES\n+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT\n+ * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,\n+ * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED\n+ * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;\n+ * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER\n+ * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN\n+ * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.\n+ *\n+ * Based on work from iobio: https://github.com/iobio\n+ *\n+ * This file incorporates work covered by the following copyright and permission notice:\n+ *\n+ *    The MIT License (MIT)\n+ *\n+ *    Copyright (c) <2014>\n+ *\n+ *    Permission is hereby granted, free of charge, to any person obtaining a copy of this software and\n+ *    associated documentation files (the \"Software\"), to deal in the Software without restriction,\n+ *    including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense,\n+ *    and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so,\n+ *    subject to the following conditions:\n+ *\n+ *    The above copyright notice and this permission notice shall be included\n+ *    in all copies or substantial portions of the Software.\n+ *\n+ *    THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO\n+ *    THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n+ *    AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,\n+ *    TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE\n+ *    SOFTWARE.\n+ */\n+\n+//\n+//  vcfiobio\n+//  Tony Di Sera\n+//  October 2014\n+//\n+//  This is a data manager class for the variant summary data.\n+// \n+//  Two file are used to generate the variant data: \n+//    1. the bgzipped vcf (.vcf.gz) \n+//    2. its corresponding tabix file (.vcf.gz.tbi).  \n+//\n+//  The variant summary data come in 3 main forms:  \n+//    1. reference names and lengths \n+//    2. variant density (point data), \n+//    3. vcf stats (variant types, tstv ration allele frequency, mutation spectrum,\n+//       insertion/deletion distribution, and qc distribution).  \n+//  The reference names and lengths as well as the variant density data obtained from \n+//  the tabix file; the vcf stats are determined by parsing the vcf file in sampled regions.\n+//\n+//  The files can be hosted remotely, specified by a URL, or reside on the client, accesssed as a local\n+//  file on the file system. When the files are on a remote server, vcfiobio communicates with iobio services \n+//  to obtain the metrics data.  When the files are accessed locally, a client-side javascript library\n+//  is used to a) read the tabix file to obtain the reference names/lengths and the variant density data \n+//  and b) parse the vcf records from sampled regions.  This mini vcf file is then streamed to iobio services\n+//  to obtain the vcf metrics.  \n+//  \n+//  The follow example code illustrates the method calls to make\n+//  when the vcf file is served remotely (a URL is entered)\n+//\n+//  var vcfiobio = vcfiobio();\n+//  vcfiobio.loadRemoteIndex(vcfUrl, function(data) {\n+//     // Filter out the short (<1% median reference length) references\n+//     vcfiobio.getReferenceData(.01, 100);\n+//     // Show all the references (example: in a pie chart) here....\n+//     // Render the variant density data here....\n+//  });\n+//  vcfiobio.getEstimatedDensity(refName);\n+//  vcfiobio.getStats(refs, options, function(data) {\n+//     // Render the vcf stats here....\n+//  });\n+//  \n+//\n+//  When the vcf file resides on the local file system, call\n+//  openVcfFile() and then call loadIndex() instead\n+//  of loadRemoteIndex().\n+//\n+//  var vcfiobio = vcfiobio();\n+//  vcfiobio.openVcfFile( event, function(vcfFile) {\n+//    vcfiobio.loadIndex( function(data) {\n+//     .... same as above ......\n+//    });\n+//  });\n+//  ...  same as above\n+//\n+//\n+Vcfiobio = function() {\n+\n+  var debug =  false;\n+\n+  var exports = {};\n+\n+  var dispatch = d3.dispatch( 'dataReady', 'dataLoading');\n+\n+  var SOURCE_TYPE_URL = \"URL\";\n+  var SOURCE_TYPE_FILE = \"file\";\n+  var sourceType = \"url\";\n+\n+  var refLengths_GRCh37 = \n+  {\n+        \"1\":   +249250621,","path":"dcc-portal-ui/app/vendor/scripts/vcfiobio/vcf.iobio.js","position":111,"original_position":111,"commit_id":"3501ef0fb3d6d205e013d986f91624deb181a2ed","original_commit_id":"3501ef0fb3d6d205e013d986f91624deb181a2ed","user":{"login":"mikecules","id":999402,"avatar_url":"https://avatars.githubusercontent.com/u/999402?v=3","gravatar_id":"","url":"https://api.github.com/users/mikecules","html_url":"https://github.com/mikecules","followers_url":"https://api.github.com/users/mikecules/followers","following_url":"https://api.github.com/users/mikecules/following{/other_user}","gists_url":"https://api.github.com/users/mikecules/gists{/gist_id}","starred_url":"https://api.github.com/users/mikecules/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mikecules/subscriptions","organizations_url":"https://api.github.com/users/mikecules/orgs","repos_url":"https://api.github.com/users/mikecules/repos","events_url":"https://api.github.com/users/mikecules/events{/privacy}","received_events_url":"https://api.github.com/users/mikecules/received_events","type":"User","site_admin":false},"body":"Is the type coercion necessary?","created_at":"2016-03-28T13:17:21Z","updated_at":"2016-03-28T13:17:21Z","html_url":"https://github.com/icgc-dcc/dcc-portal/pull/11#discussion_r57570148","pull_request_url":"https://api.github.com/repos/icgc-dcc/dcc-portal/pulls/11","_links":{"self":{"href":"https://api.github.com/repos/icgc-dcc/dcc-portal/pulls/comments/57570148"},"html":{"href":"https://github.com/icgc-dcc/dcc-portal/pull/11#discussion_r57570148"},"pull_request":{"href":"https://api.github.com/repos/icgc-dcc/dcc-portal/pulls/11"}}},"pull_request":{"url":"https://api.github.com/repos/icgc-dcc/dcc-portal/pulls/11","id":63722648,"html_url":"https://github.com/icgc-dcc/dcc-portal/pull/11","diff_url":"https://github.com/icgc-dcc/dcc-portal/pull/11.diff","patch_url":"https://github.com/icgc-dcc/dcc-portal/pull/11.patch","issue_url":"https://api.github.com/repos/icgc-dcc/dcc-portal/issues/11","number":11,"state":"open","locked":false,"title":"Feature/dcc 4443 vcf iobio viewer","user":{"login":"andricDu","id":6350043,"avatar_url":"https://avatars.githubusercontent.com/u/6350043?v=3","gravatar_id":"","url":"https://api.github.com/users/andricDu","html_url":"https://github.com/andricDu","followers_url":"https://api.github.com/users/andricDu/followers","following_url":"https://api.github.com/users/andricDu/following{/other_user}","gists_url":"https://api.github.com/users/andricDu/gists{/gist_id}","starred_url":"https://api.github.com/users/andricDu/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/andricDu/subscriptions","organizations_url":"https://api.github.com/users/andricDu/orgs","repos_url":"https://api.github.com/users/andricDu/repos","events_url":"https://api.github.com/users/andricDu/events{/privacy}","received_events_url":"https://api.github.com/users/andricDu/received_events","type":"User","site_admin":false},"body":"Opening PR for testing. \r\n\r\nVCF stats is viewable for Collab and AWS-Virginia VCF files. Viewable both in File Entity page as well as a modal by clicking the stats icon in the stats column in External Repository page. 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