{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/hellbender/pulls/comments/35026389","id":35026389,"diff_hunk":"@@ -0,0 +1,246 @@\n+package org.broadinstitute.hellbender.tools.walkers.filters;\n+\n+import org.broadinstitute.hellbender.CommandLineProgramTest;\n+import org.broadinstitute.hellbender.exceptions.UserException;\n+import org.broadinstitute.hellbender.tools.IntegrationTestSpec;\n+import org.testng.annotations.Test;\n+\n+import java.io.IOException;\n+import java.util.Arrays;\n+import java.util.Collections;\n+\n+import static org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants.ValidationType.ALL;\n+\n+public final class VariantFiltrationIntegrationTest extends CommandLineProgramTest {\n+\n+    public String baseTestString(final String vcf, final String options) {\n+        final String file = getToolTestDataDir() + vcf;\n+        return \"--variant \" + file + \" \" + options + \" -O %s\" + \" -R\" + hg19_chr1_1M_Reference;\n+    }\n+\n+    @Test\n+    public void testNoAction() throws IOException {\n+        final IntegrationTestSpec spec = new IntegrationTestSpec(\n+                baseTestString(\"vcfexample2.vcf\", \"\"),//\"-L 1:10,020,000-10,021,000\"\n+                Arrays.asList(getToolTestDataDir() + \"expected/\" + \"testVariantFiltration_testNoAction.vcf\")\n+        );\n+\n+        spec.executeTest(\"test good file\", this);\n+    }\n+\n+    @Test\n+    public void testClusteredSnps() throws IOException {\n+        final IntegrationTestSpec spec = new IntegrationTestSpec(\n+        baseTestString(\"vcfexample2.vcf\", \" -window 10 \"),\n+                Arrays.asList(getToolTestDataDir() + \"expected/\" + \"testVariantFiltration_testClusteredSnps.vcf\")\n+        );\n+\n+        spec.executeTest(\"test testClusteredSnps file\", this);\n+    }\n+\n+    @Test\n+    public void testMask1() throws IOException {\n+        final IntegrationTestSpec spec = new IntegrationTestSpec(\n+                baseTestString(\"vcfexample2.vcf\", \" -maskName foo --mask \" + getToolTestDataDir() + \"vcfexample2.vcf\"),\n+                Arrays.asList(getToolTestDataDir() + \"expected/\" + \"testVariantFiltration_testMask1.vcf\")\n+        );\n+\n+        spec.executeTest(\"test file\", this);\n+    }\n+\n+    @Test\n+    public void testMask2() throws IOException {\n+        final IntegrationTestSpec spec = new IntegrationTestSpec(\n+                baseTestString(\"vcfexample2.vcf\", \" -maskName foo --mask VCF:\" + getToolTestDataDir() + \"vcfMask.vcf\"),\n+                Arrays.asList(getToolTestDataDir() + \"expected/\" + \"testVariantFiltration_testMask2.vcf\")\n+        );\n+\n+        spec.executeTest(\"test file\", this);\n+    }\n+\n+    @Test\n+    public void testMask3() throws IOException {\n+        final IntegrationTestSpec spec = new IntegrationTestSpec(\n+                baseTestString(\"vcfexample2.vcf\", \" -maskName foo -maskExtend 10 --mask VCF:\" + getToolTestDataDir() + \"vcfMask.vcf\"),\n+                Arrays.asList(getToolTestDataDir() + \"expected/\" + \"testVariantFiltration_testMask3.vcf\")\n+        );\n+\n+        spec.executeTest(\"test file\", this);\n+    }\n+\n+\n+    @Test\n+    public void testMaskReversed() throws IOException {\n+        final IntegrationTestSpec spec = new IntegrationTestSpec(\n+                baseTestString(\"vcfexample2.vcf\", \" -maskName outsideGoodSites -filterNotInMask --mask BED:\" + getToolTestDataDir() + \"goodMask.bed\"),\n+                Arrays.asList(getToolTestDataDir() + \"expected/\" + \"testVariantFiltration_testMaskReversed.vcf\")\n+        );\n+\n+        spec.executeTest(\"test file\", this);\n+    }\n+\n+    @Test\n+    public void testIllegalFilterName() throws IOException {\n+        final IntegrationTestSpec spec = new IntegrationTestSpec(\n+                baseTestString(\"vcfexample2.vcf\", \" -filter 'DoC < 20 || FisherStrand > 20.0' -filterName 'foo < foo' \"),\n+                1,\n+                UserException.class\n+        );\n+\n+        spec.executeTest(\"test file\", this);\n+    }\n+\n+    @Test\n+    public void testFilter1() throws IOException {\n+        final IntegrationTestSpec spec = new IntegrationTestSpec(\n+                baseTestString(\"vcfexample2.vcf\", \" -filter 'DoC < 20 || FisherStrand > 20.0' -filterName foo \"),\n+                Arrays.asList(getToolTestDataDir() + \"expected/\" + \"testVariantFiltration_testFilter1.vcf\")\n+        );\n+\n+        spec.executeTest(\"test file\", this);\n+    }\n+\n+    @Test\n+    public void testFilter2() throws IOException {\n+        final IntegrationTestSpec spec = new IntegrationTestSpec(\n+                baseTestString(\"vcfexample2.vcf\", \" -filter 'AlleleBalance < 70.0 && FisherStrand == 1.4' -filterName bar \"),\n+                Arrays.asList(getToolTestDataDir() + \"expected/\" + \"testVariantFiltration_testFilter2.vcf\")\n+        );\n+\n+        spec.executeTest(\"test file\", this);\n+    }\n+\n+    @Test\n+    public void testFilterWithSeparateNames() throws IOException {\n+        final IntegrationTestSpec spec = new IntegrationTestSpec(\n+                baseTestString(\"vcfexample2.vcf\", \" --filterName ABF -filter 'AlleleBalance < 0.7' --filterName FSF -filter 'FisherStrand == 1.4' \"),\n+                Arrays.asList(getToolTestDataDir() + \"expected/\" + \"testVariantFiltration_testFilterWithSeparateNames.vcf\")\n+        );\n+\n+        spec.executeTest(\"test file\", this);\n+    }\n+\n+    @Test\n+    public void testInvertFilter() throws IOException {\n+        final IntegrationTestSpec spec = new IntegrationTestSpec(\n+                baseTestString(\"vcfexample2.vcf\", \" --filterName ABF -filter 'AlleleBalance < 0.7' --filterName FSF -filter 'FisherStrand == 1.4' --invertFilterExpression \"),\n+                Arrays.asList(getToolTestDataDir() + \"expected/\" + \"testVariantFiltration_testInvertFilter.vcf\")\n+        );\n+\n+        spec.executeTest(\"test file\", this);\n+    }\n+\n+    @Test\n+    public void testInvertJexlFilter() throws IOException {\n+        final IntegrationTestSpec spec = new IntegrationTestSpec(\n+                baseTestString(\"vcfexample2.vcf\", \" --filterName ABF -filter 'AlleleBalance >= 0.7' --filterName FSF -filter 'FisherStrand != 1.4' \"),\n+                Arrays.asList(getToolTestDataDir() + \"expected/\" + \"testVariantFiltration_testInvertJexlFilter.vcf\")\n+        );\n+\n+        spec.executeTest(\"test file\", this);\n+    }\n+\n+    @Test\n+    public void testGenotypeFilters1() throws IOException {\n+        final IntegrationTestSpec spec = new IntegrationTestSpec(\n+                baseTestString(\"vcfexample2.vcf\", \" -G_filter 'GQ == 0.60' -G_filterName foo \"),\n+                Arrays.asList(getToolTestDataDir() + \"expected/\" + \"testVariantFiltration_testGenotypeFilters1.vcf\")\n+        );\n+\n+        spec.executeTest(\"test file\", this);\n+    }\n+\n+    @Test\n+    public void testGenotypeFilters2() throws IOException {\n+        final IntegrationTestSpec spec = new IntegrationTestSpec(\n+                baseTestString(\"vcfexample2.vcf\", \" -G_filter 'isHomVar == 1' -G_filterName foo \"),\n+                Arrays.asList(getToolTestDataDir() + \"expected/\" + \"testVariantFiltration_testGenotypeFilters2.vcf\")\n+        );\n+\n+        spec.executeTest(\"test file\", this);\n+    }\n+\n+    @Test\n+    public void testDeletions() throws IOException {\n+        final IntegrationTestSpec spec = new IntegrationTestSpec(\n+                baseTestString(\"twoDeletions.vcf\", \" --filterExpression 'QUAL < 100' --filterName foo \"),\n+                Arrays.asList(getToolTestDataDir() + \"expected/\" + \"testVariantFiltration_testDeletions.vcf\")\n+        );\n+\n+        spec.executeTest(\"test file\", this);\n+    }\n+\n+    @Test\n+    public void testUnfilteredBecomesFilteredAndPass() throws IOException {\n+        final IntegrationTestSpec spec = new IntegrationTestSpec(\n+                baseTestString(\"unfilteredForFiltering.vcf\", \" --filterExpression 'FS > 60.0' --filterName SNP_FS \"),\n+                Arrays.asList(getToolTestDataDir() + \"expected/\" + \"testVariantFiltration_testUnfilteredBecomesFilteredAndPass.vcf\")\n+        );\n+\n+        spec.executeTest(\"test file\", this);\n+    }\n+\n+    @Test\n+    public void testFilteringDPfromINFO() throws IOException {\n+        final IntegrationTestSpec spec = new IntegrationTestSpec(\n+                baseTestString(\"filteringDepthInFormat.vcf\", \" --filterExpression 'DP < 8' --filterName lowDP \"),\n+                Arrays.asList(getToolTestDataDir() + \"expected/\" + \"testVariantFiltration_testFilteringDPfromINFO.vcf\")\n+        );\n+\n+        spec.executeTest(\"test file\", this);\n+    }\n+\n+    @Test\n+    public void testFilteringDPfromFORMAT() throws IOException {\n+        final IntegrationTestSpec spec = new IntegrationTestSpec(\n+                baseTestString(\"filteringDepthInFormat.vcf\", \" -genotypeFilterExpression 'DP < 8' --genotypeFilterName lowDP \"),\n+                Arrays.asList(getToolTestDataDir() + \"expected/\" + \"testVariantFiltration_testFilteringDPfromFORMAT.vcf\")\n+        );\n+\n+        spec.executeTest(\"test file\", this);\n+    }\n+\n+    @Test\n+    public void testInvertGenotypeFilterExpression() throws IOException {\n+        final IntegrationTestSpec spec = new IntegrationTestSpec(\n+                baseTestString(\"filteringDepthInFormat.vcf\", \" --genotypeFilterExpression 'DP < 8' --genotypeFilterName highDP --invertGenotypeFilterExpression \"),\n+                Arrays.asList(getToolTestDataDir() + \"expected/\" + \"testVariantFiltration_testInvertGenotypeFilterExpression.vcf\")\n+        );\n+\n+        spec.executeTest(\"test file\", this);\n+    }\n+\n+    @Test\n+    public void testInvertJexlGenotypeFilterExpression() throws IOException {\n+        final IntegrationTestSpec spec = new IntegrationTestSpec(\n+                baseTestString(\"filteringDepthInFormat.vcf\", \" --genotypeFilterExpression 'DP >= 8' --genotypeFilterName highDP \"),\n+                Arrays.asList(getToolTestDataDir() + \"expected/\" + \"testVariantFiltration_testInvertJexlGenotypeFilterExpression.vcf\")\n+        );","path":"src/test/java/org/broadinstitute/hellbender/tools/walkers/filters/VariantFiltrationIntegrationTest.java","position":218,"original_position":218,"commit_id":"e8c266ec99b02010852b860be6dbe080d5bfad4a","original_commit_id":"e8c266ec99b02010852b860be6dbe080d5bfad4a","user":{"login":"akiezun","id":1993519,"avatar_url":"https://avatars.githubusercontent.com/u/1993519?v=3","gravatar_id":"","url":"https://api.github.com/users/akiezun","html_url":"https://github.com/akiezun","followers_url":"https://api.github.com/users/akiezun/followers","following_url":"https://api.github.com/users/akiezun/following{/other_user}","gists_url":"https://api.github.com/users/akiezun/gists{/gist_id}","starred_url":"https://api.github.com/users/akiezun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/akiezun/subscriptions","organizations_url":"https://api.github.com/users/akiezun/orgs","repos_url":"https://api.github.com/users/akiezun/repos","events_url":"https://api.github.com/users/akiezun/events{/privacy}","received_events_url":"https://api.github.com/users/akiezun/received_events","type":"User","site_admin":false},"body":"clarified it now","created_at":"2015-07-20T18:22:46Z","updated_at":"2015-07-20T18:22:46Z","html_url":"https://github.com/broadinstitute/hellbender/pull/614#discussion_r35026389","pull_request_url":"https://api.github.com/repos/broadinstitute/hellbender/pulls/614","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/hellbender/pulls/comments/35026389"},"html":{"href":"https://github.com/broadinstitute/hellbender/pull/614#discussion_r35026389"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/hellbender/pulls/614"}}},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/hellbender/pulls/614","id":39312400,"html_url":"https://github.com/broadinstitute/hellbender/pull/614","diff_url":"https://github.com/broadinstitute/hellbender/pull/614.diff","patch_url":"https://github.com/broadinstitute/hellbender/pull/614.patch","issue_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/614","number":614,"state":"open","locked":false,"title":"VariantFiltration - port and a ~half-rewrite for GATK4. ","user":{"login":"akiezun","id":1993519,"avatar_url":"https://avatars.githubusercontent.com/u/1993519?v=3","gravatar_id":"","url":"https://api.github.com/users/akiezun","html_url":"https://github.com/akiezun","followers_url":"https://api.github.com/users/akiezun/followers","following_url":"https://api.github.com/users/akiezun/following{/other_user}","gists_url":"https://api.github.com/users/akiezun/gists{/gist_id}","starred_url":"https://api.github.com/users/akiezun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/akiezun/subscriptions","organizations_url":"https://api.github.com/users/akiezun/orgs","repos_url":"https://api.github.com/users/akiezun/repos","events_url":"https://api.github.com/users/akiezun/events{/privacy}","received_events_url":"https://api.github.com/users/akiezun/received_events","type":"User","site_admin":false},"body":"It is now site-by-site independent (unlike GATK3).\r\n\r\nAll integration tests were ported as is (after ditching the MD5s). The algorithm was changed so that it works on a site-by-site independent basis. Some changes to the engine classes were required to allow queries over intervals in feature data sources.\r\n\r\nFixes https://github.com/broadinstitute/hellbender/issues/38","created_at":"2015-07-06T21:24:06Z","updated_at":"2015-07-20T18:22:46Z","closed_at":null,"merged_at":null,"merge_commit_sha":"bb470a954cf6e2dec8080eaefe12e445647e8afc","assignee":{"login":"akiezun","id":1993519,"avatar_url":"https://avatars.githubusercontent.com/u/1993519?v=3","gravatar_id":"","url":"https://api.github.com/users/akiezun","html_url":"https://github.com/akiezun","followers_url":"https://api.github.com/users/akiezun/followers","following_url":"https://api.github.com/users/akiezun/following{/other_user}","gists_url":"https://api.github.com/users/akiezun/gists{/gist_id}","starred_url":"https://api.github.com/users/akiezun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/akiezun/subscriptions","organizations_url":"https://api.github.com/users/akiezun/orgs","repos_url":"https://api.github.com/users/akiezun/repos","events_url":"https://api.github.com/users/akiezun/events{/privacy}","received_events_url":"https://api.github.com/users/akiezun/received_events","type":"User","site_admin":false},"milestone":null,"commits_url":"https://api.github.com/repos/broadinstitute/hellbender/pulls/614/commits","review_comments_url":"https://api.github.com/repos/broadinstitute/hellbender/pulls/614/comments","review_comment_url":"https://api.github.com/repos/broadinstitute/hellbender/pulls/comments{/number}","comments_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/614/comments","statuses_url":"https://api.github.com/repos/broadinstitute/hellbender/statuses/e8c266ec99b02010852b860be6dbe080d5bfad4a","head":{"label":"broadinstitute:ak_variant_filtration","ref":"ak_variant_filtration","sha":"e8c266ec99b02010852b860be6dbe080d5bfad4a","user":{"login":"broadinstitute","id":393552,"avatar_url":"https://avatars.githubusercontent.com/u/393552?v=3","gravatar_id":"","url":"https://api.github.com/users/broadinstitute","html_url":"https://github.com/broadinstitute","followers_url":"https://api.github.com/users/broadinstitute/followers","following_url":"https://api.github.com/users/broadinstitute/following{/other_user}","gists_url":"https://api.github.com/users/broadinstitute/gists{/gist_id}","starred_url":"https://api.github.com/users/broadinstitute/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/broadinstitute/subscriptions","organizations_url":"https://api.github.com/users/broadinstitute/orgs","repos_url":"https://api.github.com/users/broadinstitute/repos","events_url":"https://api.github.com/users/broadinstitute/events{/privacy}","received_events_url":"https://api.github.com/users/broadinstitute/received_events","type":"Organization","site_admin":false},"repo":{"id":27452807,"name":"hellbender","full_name":"broadinstitute/hellbender","owner":{"login":"broadinstitute","id":393552,"avatar_url":"https://avatars.githubusercontent.com/u/393552?v=3","gravatar_id":"","url":"https://api.github.com/users/broadinstitute","html_url":"https://github.com/broadinstitute","followers_url":"https://api.github.com/users/broadinstitute/followers","following_url":"https://api.github.com/users/broadinstitute/following{/other_user}","gists_url":"https://api.github.com/users/broadinstitute/gists{/gist_id}","starred_url":"https://api.github.com/users/broadinstitute/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/broadinstitute/subscriptions","organizations_url":"https://api.github.com/users/broadinstitute/orgs","repos_url":"https://api.github.com/users/broadinstitute/repos","events_url":"https://api.github.com/users/broadinstitute/events{/privacy}","received_events_url":"https://api.github.com/users/broadinstitute/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/broadinstitute/hellbender","description":"GATK4 development","fork":false,"url":"https://api.github.com/repos/broadinstitute/hellbender","forks_url":"https://api.github.com/repos/broadinstitute/hellbender/forks","keys_url":"https://api.github.com/repos/broadinstitute/hellbender/keys{/key_id}","collaborators_url":"https://api.github.com/repos/broadinstitute/hellbender/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/broadinstitute/hellbender/teams","hooks_url":"https://api.github.com/repos/broadinstitute/hellbender/hooks","issue_events_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/events{/number}","events_url":"https://api.github.com/repos/broadinstitute/hellbender/events","assignees_url":"https://api.github.com/repos/broadinstitute/hellbender/assignees{/user}","branches_url":"https://api.github.com/repos/broadinstitute/hellbender/branches{/branch}","tags_url":"https://api.github.com/repos/broadinstitute/hellbender/tags","blobs_url":"https://api.github.com/repos/broadinstitute/hellbender/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/broadinstitute/hellbender/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/broadinstitute/hellbender/git/refs{/sha}","trees_url":"https://api.github.com/repos/broadinstitute/hellbender/git/trees{/sha}","statuses_url":"https://api.github.com/repos/broadinstitute/hellbender/statuses/{sha}","languages_url":"https://api.github.com/repos/broadinstitute/hellbender/languages","stargazers_url":"https://api.github.com/repos/broadinstitute/hellbender/stargazers","contributors_url":"https://api.github.com/repos/broadinstitute/hellbender/contributors","subscribers_url":"https://api.github.com/repos/broadinstitute/hellbender/subscribers","subscription_url":"https://api.github.com/repos/broadinstitute/hellbender/subscription","commits_url":"https://api.github.com/repos/broadinstitute/hellbender/commits{/sha}","git_commits_url":"https://api.github.com/repos/broadinstitute/hellbender/git/commits{/sha}","comments_url":"https://api.github.com/repos/broadinstitute/hellbender/comments{/number}","issue_comment_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/comments{/number}","contents_url":"https://api.github.com/repos/broadinstitute/hellbender/contents/{+path}","compare_url":"https://api.github.com/repos/broadinstitute/hellbender/compare/{base}...{head}","merges_url":"https://api.github.com/repos/broadinstitute/hellbender/merges","archive_url":"https://api.github.com/repos/broadinstitute/hellbender/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/broadinstitute/hellbender/downloads","issues_url":"https://api.github.com/repos/broadinstitute/hellbender/issues{/number}","pulls_url":"https://api.github.com/repos/broadinstitute/hellbender/pulls{/number}","milestones_url":"https://api.github.com/repos/broadinstitute/hellbender/milestones{/number}","notifications_url":"https://api.github.com/repos/broadinstitute/hellbender/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/broadinstitute/hellbender/labels{/name}","releases_url":"https://api.github.com/repos/broadinstitute/hellbender/releases{/id}","created_at":"2014-12-02T20:50:36Z","updated_at":"2015-07-05T14:31:29Z","pushed_at":"2015-07-20T16:45:38Z","git_url":"git://github.com/broadinstitute/hellbender.git","ssh_url":"git@github.com:broadinstitute/hellbender.git","clone_url":"https://github.com/broadinstitute/hellbender.git","svn_url":"https://github.com/broadinstitute/hellbender","homepage":"","size":32857,"stargazers_count":26,"watchers_count":26,"language":"Java","has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":6,"mirror_url":null,"open_issues_count":211,"forks":6,"open_issues":211,"watchers":26,"default_branch":"master"}},"base":{"label":"broadinstitute:master","ref":"master","sha":"9a3044247b8a18bdb6df8dfa1f76e0ce27fe8c2f","user":{"login":"broadinstitute","id":393552,"avatar_url":"https://avatars.githubusercontent.com/u/393552?v=3","gravatar_id":"","url":"https://api.github.com/users/broadinstitute","html_url":"https://github.com/broadinstitute","followers_url":"https://api.github.com/users/broadinstitute/followers","following_url":"https://api.github.com/users/broadinstitute/following{/other_user}","gists_url":"https://api.github.com/users/broadinstitute/gists{/gist_id}","starred_url":"https://api.github.com/users/broadinstitute/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/broadinstitute/subscriptions","organizations_url":"https://api.github.com/users/broadinstitute/orgs","repos_url":"https://api.github.com/users/broadinstitute/repos","events_url":"https://api.github.com/users/broadinstitute/events{/privacy}","received_events_url":"https://api.github.com/users/broadinstitute/received_events","type":"Organization","site_admin":false},"repo":{"id":27452807,"name":"hellbender","full_name":"broadinstitute/hellbender","owner":{"login":"broadinstitute","id":393552,"avatar_url":"https://avatars.githubusercontent.com/u/393552?v=3","gravatar_id":"","url":"https://api.github.com/users/broadinstitute","html_url":"https://github.com/broadinstitute","followers_url":"https://api.github.com/users/broadinstitute/followers","following_url":"https://api.github.com/users/broadinstitute/following{/other_user}","gists_url":"https://api.github.com/users/broadinstitute/gists{/gist_id}","starred_url":"https://api.github.com/users/broadinstitute/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/broadinstitute/subscriptions","organizations_url":"https://api.github.com/users/broadinstitute/orgs","repos_url":"https://api.github.com/users/broadinstitute/repos","events_url":"https://api.github.com/users/broadinstitute/events{/privacy}","received_events_url":"https://api.github.com/users/broadinstitute/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/broadinstitute/hellbender","description":"GATK4 development","fork":false,"url":"https://api.github.com/repos/broadinstitute/hellbender","forks_url":"https://api.github.com/repos/broadinstitute/hellbender/forks","keys_url":"https://api.github.com/repos/broadinstitute/hellbender/keys{/key_id}","collaborators_url":"https://api.github.com/repos/broadinstitute/hellbender/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/broadinstitute/hellbender/teams","hooks_url":"https://api.github.com/repos/broadinstitute/hellbender/hooks","issue_events_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/events{/number}","events_url":"https://api.github.com/repos/broadinstitute/hellbender/events","assignees_url":"https://api.github.com/repos/broadinstitute/hellbender/assignees{/user}","branches_url":"https://api.github.com/repos/broadinstitute/hellbender/branches{/branch}","tags_url":"https://api.github.com/repos/broadinstitute/hellbender/tags","blobs_url":"https://api.github.com/repos/broadinstitute/hellbender/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/broadinstitute/hellbender/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/broadinstitute/hellbender/git/refs{/sha}","trees_url":"https://api.github.com/repos/broadinstitute/hellbender/git/trees{/sha}","statuses_url":"https://api.github.com/repos/broadinstitute/hellbender/statuses/{sha}","languages_url":"https://api.github.com/repos/broadinstitute/hellbender/languages","stargazers_url":"https://api.github.com/repos/broadinstitute/hellbender/stargazers","contributors_url":"https://api.github.com/repos/broadinstitute/hellbender/contributors","subscribers_url":"https://api.github.com/repos/broadinstitute/hellbender/subscribers","subscription_url":"https://api.github.com/repos/broadinstitute/hellbender/subscription","commits_url":"https://api.github.com/repos/broadinstitute/hellbender/commits{/sha}","git_commits_url":"https://api.github.com/repos/broadinstitute/hellbender/git/commits{/sha}","comments_url":"https://api.github.com/repos/broadinstitute/hellbender/comments{/number}","issue_comment_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/comments{/number}","contents_url":"https://api.github.com/repos/broadinstitute/hellbender/contents/{+path}","compare_url":"https://api.github.com/repos/broadinstitute/hellbender/compare/{base}...{head}","merges_url":"https://api.github.com/repos/broadinstitute/hellbender/merges","archive_url":"https://api.github.com/repos/broadinstitute/hellbender/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/broadinstitute/hellbender/downloads","issues_url":"https://api.github.com/repos/broadinstitute/hellbender/issues{/number}","pulls_url":"https://api.github.com/repos/broadinstitute/hellbender/pulls{/number}","milestones_url":"https://api.github.com/repos/broadinstitute/hellbender/milestones{/number}","notifications_url":"https://api.github.com/repos/broadinstitute/hellbender/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/broadinstitute/hellbender/labels{/name}","releases_url":"https://api.github.com/repos/broadinstitute/hellbender/releases{/id}","created_at":"2014-12-02T20:50:36Z","updated_at":"2015-07-05T14:31:29Z","pushed_at":"2015-07-20T16:45:38Z","git_url":"git://github.com/broadinstitute/hellbender.git","ssh_url":"git@github.com:broadinstitute/hellbender.git","clone_url":"https://github.com/broadinstitute/hellbender.git","svn_url":"https://github.com/broadinstitute/hellbender","homepage":"","size":32857,"stargazers_count":26,"watchers_count":26,"language":"Java","has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":6,"mirror_url":null,"open_issues_count":211,"forks":6,"open_issues":211,"watchers":26,"default_branch":"master"}},"_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/hellbender/pulls/614"},"html":{"href":"https://github.com/broadinstitute/hellbender/pull/614"},"issue":{"href":"https://api.github.com/repos/broadinstitute/hellbender/issues/614"},"comments":{"href":"https://api.github.com/repos/broadinstitute/hellbender/issues/614/comments"},"review_comments":{"href":"https://api.github.com/repos/broadinstitute/hellbender/pulls/614/comments"},"review_comment":{"href":"https://api.github.com/repos/broadinstitute/hellbender/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/broadinstitute/hellbender/pulls/614/commits"},"statuses":{"href":"https://api.github.com/repos/broadinstitute/hellbender/statuses/e8c266ec99b02010852b860be6dbe080d5bfad4a"}}}}