{"action":"closed","number":13,"pull_request":{"url":"https://api.github.com/repos/jimhester/primerTree/pulls/13","id":32987933,"html_url":"https://github.com/jimhester/primerTree/pull/13","diff_url":"https://github.com/jimhester/primerTree/pull/13.diff","patch_url":"https://github.com/jimhester/primerTree/pull/13.patch","issue_url":"https://api.github.com/repos/jimhester/primerTree/issues/13","number":13,"state":"closed","locked":false,"title":"Using pairwise deletion when calculating distance matrix","user":{"login":"MVesuviusC","id":5831817,"avatar_url":"https://avatars.githubusercontent.com/u/5831817?v=3","gravatar_id":"","url":"https://api.github.com/users/MVesuviusC","html_url":"https://github.com/MVesuviusC","followers_url":"https://api.github.com/users/MVesuviusC/followers","following_url":"https://api.github.com/users/MVesuviusC/following{/other_user}","gists_url":"https://api.github.com/users/MVesuviusC/gists{/gist_id}","starred_url":"https://api.github.com/users/MVesuviusC/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MVesuviusC/subscriptions","organizations_url":"https://api.github.com/users/MVesuviusC/orgs","repos_url":"https://api.github.com/users/MVesuviusC/repos","events_url":"https://api.github.com/users/MVesuviusC/events{/privacy}","received_events_url":"https://api.github.com/users/MVesuviusC/received_events","type":"User","site_admin":false},"body":"I changed the dist.dna function to calculate pairwise deletions by default to fix an issue where very divergent sequences retrieved from blast can result in an empty distance matrix and a tree with zero tips. ex: plot(search_primer_pair(name=\"Archaea 16S\",\"CCGACGGTGAGRGRYGAA\",\"GTGCTCCCCCGCCAATTCCT\",num_aligns=1000))","created_at":"2015-04-09T19:28:37Z","updated_at":"2015-04-10T14:07:05Z","closed_at":"2015-04-10T14:07:04Z","merged_at":"2015-04-10T14:07:04Z","merge_commit_sha":"36262b6ab1cc392cc2b27fb2b5fc6051ffd3d908","assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/jimhester/primerTree/pulls/13/commits","review_comments_url":"https://api.github.com/repos/jimhester/primerTree/pulls/13/comments","review_comment_url":"https://api.github.com/repos/jimhester/primerTree/pulls/comments{/number}","comments_url":"https://api.github.com/repos/jimhester/primerTree/issues/13/comments","statuses_url":"https://api.github.com/repos/jimhester/primerTree/statuses/7c24847b5d3ede9e3635c515839025a27ab8db6a","head":{"label":"MVesuviusC:master","ref":"master","sha":"7c24847b5d3ede9e3635c515839025a27ab8db6a","user":{"login":"MVesuviusC","id":5831817,"avatar_url":"https://avatars.githubusercontent.com/u/5831817?v=3","gravatar_id":"","url":"https://api.github.com/users/MVesuviusC","html_url":"https://github.com/MVesuviusC","followers_url":"https://api.github.com/users/MVesuviusC/followers","following_url":"https://api.github.com/users/MVesuviusC/following{/other_user}","gists_url":"https://api.github.com/users/MVesuviusC/gists{/gist_id}","starred_url":"https://api.github.com/users/MVesuviusC/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MVesuviusC/subscriptions","organizations_url":"https://api.github.com/users/MVesuviusC/orgs","repos_url":"https://api.github.com/users/MVesuviusC/repos","events_url":"https://api.github.com/users/MVesuviusC/events{/privacy}","received_events_url":"https://api.github.com/users/MVesuviusC/received_events","type":"User","site_admin":false},"repo":{"id":33612774,"name":"primerTree","full_name":"MVesuviusC/primerTree","owner":{"login":"MVesuviusC","id":5831817,"avatar_url":"https://avatars.githubusercontent.com/u/5831817?v=3","gravatar_id":"","url":"https://api.github.com/users/MVesuviusC","html_url":"https://github.com/MVesuviusC","followers_url":"https://api.github.com/users/MVesuviusC/followers","following_url":"https://api.github.com/users/MVesuviusC/following{/other_user}","gists_url":"https://api.github.com/users/MVesuviusC/gists{/gist_id}","starred_url":"https://api.github.com/users/MVesuviusC/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MVesuviusC/subscriptions","organizations_url":"https://api.github.com/users/MVesuviusC/orgs","repos_url":"https://api.github.com/users/MVesuviusC/repos","events_url":"https://api.github.com/users/MVesuviusC/events{/privacy}","received_events_url":"https://api.github.com/users/MVesuviusC/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/MVesuviusC/primerTree","description":"PrimerTree: Visually Assessing the Specificity and Informativeness of Primer Pairs","fork":true,"url":"https://api.github.com/repos/MVesuviusC/primerTree","forks_url":"https://api.github.com/repos/MVesuviusC/primerTree/forks","keys_url":"https://api.github.com/repos/MVesuviusC/primerTree/keys{/key_id}","collaborators_url":"https://api.github.com/repos/MVesuviusC/primerTree/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/MVesuviusC/primerTree/teams","hooks_url":"https://api.github.com/repos/MVesuviusC/primerTree/hooks","issue_events_url":"https://api.github.com/repos/MVesuviusC/primerTree/issues/events{/number}","events_url":"https://api.github.com/repos/MVesuviusC/primerTree/events","assignees_url":"https://api.github.com/repos/MVesuviusC/primerTree/assignees{/user}","branches_url":"https://api.github.com/repos/MVesuviusC/primerTree/branches{/branch}","tags_url":"https://api.github.com/repos/MVesuviusC/primerTree/tags","blobs_url":"https://api.github.com/repos/MVesuviusC/primerTree/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/MVesuviusC/primerTree/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/MVesuviusC/primerTree/git/refs{/sha}","trees_url":"https://api.github.com/repos/MVesuviusC/primerTree/git/trees{/sha}","statuses_url":"https://api.github.com/repos/MVesuviusC/primerTree/statuses/{sha}","languages_url":"https://api.github.com/repos/MVesuviusC/primerTree/languages","stargazers_url":"https://api.github.com/repos/MVesuviusC/primerTree/stargazers","contributors_url":"https://api.github.com/repos/MVesuviusC/primerTree/contributors","subscribers_url":"https://api.github.com/repos/MVesuviusC/primerTree/subscribers","subscription_url":"https://api.github.com/repos/MVesuviusC/primerTree/subscription","commits_url":"https://api.github.com/repos/MVesuviusC/primerTree/commits{/sha}","git_commits_url":"https://api.github.com/repos/MVesuviusC/primerTree/git/commits{/sha}","comments_url":"https://api.github.com/repos/MVesuviusC/primerTree/comments{/number}","issue_comment_url":"https://api.github.com/repos/MVesuviusC/primerTree/issues/comments{/number}","contents_url":"https://api.github.com/repos/MVesuviusC/primerTree/contents/{+path}","compare_url":"https://api.github.com/repos/MVesuviusC/primerTree/compare/{base}...{head}","merges_url":"https://api.github.com/repos/MVesuviusC/primerTree/merges","archive_url":"https://api.github.com/repos/MVesuviusC/primerTree/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/MVesuviusC/primerTree/downloads","issues_url":"https://api.github.com/repos/MVesuviusC/primerTree/issues{/number}","pulls_url":"https://api.github.com/repos/MVesuviusC/primerTree/pulls{/number}","milestones_url":"https://api.github.com/repos/MVesuviusC/primerTree/milestones{/number}","notifications_url":"https://api.github.com/repos/MVesuviusC/primerTree/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/MVesuviusC/primerTree/labels{/name}","releases_url":"https://api.github.com/repos/MVesuviusC/primerTree/releases{/id}","created_at":"2015-04-08T14:42:58Z","updated_at":"2015-04-10T14:01:53Z","pushed_at":"2015-04-10T14:01:53Z","git_url":"git://github.com/MVesuviusC/primerTree.git","ssh_url":"git@github.com:MVesuviusC/primerTree.git","clone_url":"https://github.com/MVesuviusC/primerTree.git","svn_url":"https://github.com/MVesuviusC/primerTree","homepage":"","size":680,"stargazers_count":0,"watchers_count":0,"language":"R","has_issues":false,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":0,"mirror_url":null,"open_issues_count":0,"forks":0,"open_issues":0,"watchers":0,"default_branch":"master"}},"base":{"label":"jimhester:master","ref":"master","sha":"7bc8e8f6a2d881fe77ed4dd00e347df0f4a9df46","user":{"login":"jimhester","id":205275,"avatar_url":"https://avatars.githubusercontent.com/u/205275?v=3","gravatar_id":"","url":"https://api.github.com/users/jimhester","html_url":"https://github.com/jimhester","followers_url":"https://api.github.com/users/jimhester/followers","following_url":"https://api.github.com/users/jimhester/following{/other_user}","gists_url":"https://api.github.com/users/jimhester/gists{/gist_id}","starred_url":"https://api.github.com/users/jimhester/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jimhester/subscriptions","organizations_url":"https://api.github.com/users/jimhester/orgs","repos_url":"https://api.github.com/users/jimhester/repos","events_url":"https://api.github.com/users/jimhester/events{/privacy}","received_events_url":"https://api.github.com/users/jimhester/received_events","type":"User","site_admin":false},"repo":{"id":13065453,"name":"primerTree","full_name":"jimhester/primerTree","owner":{"login":"jimhester","id":205275,"avatar_url":"https://avatars.githubusercontent.com/u/205275?v=3","gravatar_id":"","url":"https://api.github.com/users/jimhester","html_url":"https://github.com/jimhester","followers_url":"https://api.github.com/users/jimhester/followers","following_url":"https://api.github.com/users/jimhester/following{/other_user}","gists_url":"https://api.github.com/users/jimhester/gists{/gist_id}","starred_url":"https://api.github.com/users/jimhester/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jimhester/subscriptions","organizations_url":"https://api.github.com/users/jimhester/orgs","repos_url":"https://api.github.com/users/jimhester/repos","events_url":"https://api.github.com/users/jimhester/events{/privacy}","received_events_url":"https://api.github.com/users/jimhester/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/jimhester/primerTree","description":"PrimerTree: Visually Assessing the Specificity and Informativeness of Primer Pairs","fork":false,"url":"https://api.github.com/repos/jimhester/primerTree","forks_url":"https://api.github.com/repos/jimhester/primerTree/forks","keys_url":"https://api.github.com/repos/jimhester/primerTree/keys{/key_id}","collaborators_url":"https://api.github.com/repos/jimhester/primerTree/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/jimhester/primerTree/teams","hooks_url":"https://api.github.com/repos/jimhester/primerTree/hooks","issue_events_url":"https://api.github.com/repos/jimhester/primerTree/issues/events{/number}","events_url":"https://api.github.com/repos/jimhester/primerTree/events","assignees_url":"https://api.github.com/repos/jimhester/primerTree/assignees{/user}","branches_url":"https://api.github.com/repos/jimhester/primerTree/branches{/branch}","tags_url":"https://api.github.com/repos/jimhester/primerTree/tags","blobs_url":"https://api.github.com/repos/jimhester/primerTree/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/jimhester/primerTree/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/jimhester/primerTree/git/refs{/sha}","trees_url":"https://api.github.com/repos/jimhester/primerTree/git/trees{/sha}","statuses_url":"https://api.github.com/repos/jimhester/primerTree/statuses/{sha}","languages_url":"https://api.github.com/repos/jimhester/primerTree/languages","stargazers_url":"https://api.github.com/repos/jimhester/primerTree/stargazers","contributors_url":"https://api.github.com/repos/jimhester/primerTree/contributors","subscribers_url":"https://api.github.com/repos/jimhester/primerTree/subscribers","subscription_url":"https://api.github.com/repos/jimhester/primerTree/subscription","commits_url":"https://api.github.com/repos/jimhester/primerTree/commits{/sha}","git_commits_url":"https://api.github.com/repos/jimhester/primerTree/git/commits{/sha}","comments_url":"https://api.github.com/repos/jimhester/primerTree/comments{/number}","issue_comment_url":"https://api.github.com/repos/jimhester/primerTree/issues/comments{/number}","contents_url":"https://api.github.com/repos/jimhester/primerTree/contents/{+path}","compare_url":"https://api.github.com/repos/jimhester/primerTree/compare/{base}...{head}","merges_url":"https://api.github.com/repos/jimhester/primerTree/merges","archive_url":"https://api.github.com/repos/jimhester/primerTree/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/jimhester/primerTree/downloads","issues_url":"https://api.github.com/repos/jimhester/primerTree/issues{/number}","pulls_url":"https://api.github.com/repos/jimhester/primerTree/pulls{/number}","milestones_url":"https://api.github.com/repos/jimhester/primerTree/milestones{/number}","notifications_url":"https://api.github.com/repos/jimhester/primerTree/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/jimhester/primerTree/labels{/name}","releases_url":"https://api.github.com/repos/jimhester/primerTree/releases{/id}","created_at":"2013-09-24T13:40:44Z","updated_at":"2015-04-09T15:49:25Z","pushed_at":"2015-04-10T14:07:04Z","git_url":"git://github.com/jimhester/primerTree.git","ssh_url":"git@github.com:jimhester/primerTree.git","clone_url":"https://github.com/jimhester/primerTree.git","svn_url":"https://github.com/jimhester/primerTree","homepage":"","size":793,"stargazers_count":2,"watchers_count":2,"language":"R","has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":2,"mirror_url":null,"open_issues_count":2,"forks":2,"open_issues":2,"watchers":2,"default_branch":"master"}},"_links":{"self":{"href":"https://api.github.com/repos/jimhester/primerTree/pulls/13"},"html":{"href":"https://github.com/jimhester/primerTree/pull/13"},"issue":{"href":"https://api.github.com/repos/jimhester/primerTree/issues/13"},"comments":{"href":"https://api.github.com/repos/jimhester/primerTree/issues/13/comments"},"review_comments":{"href":"https://api.github.com/repos/jimhester/primerTree/pulls/13/comments"},"review_comment":{"href":"https://api.github.com/repos/jimhester/primerTree/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/jimhester/primerTree/pulls/13/commits"},"statuses":{"href":"https://api.github.com/repos/jimhester/primerTree/statuses/7c24847b5d3ede9e3635c515839025a27ab8db6a"}},"merged":true,"mergeable":null,"mergeable_state":"unknown","merged_by":{"login":"jimhester","id":205275,"avatar_url":"https://avatars.githubusercontent.com/u/205275?v=3","gravatar_id":"","url":"https://api.github.com/users/jimhester","html_url":"https://github.com/jimhester","followers_url":"https://api.github.com/users/jimhester/followers","following_url":"https://api.github.com/users/jimhester/following{/other_user}","gists_url":"https://api.github.com/users/jimhester/gists{/gist_id}","starred_url":"https://api.github.com/users/jimhester/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jimhester/subscriptions","organizations_url":"https://api.github.com/users/jimhester/orgs","repos_url":"https://api.github.com/users/jimhester/repos","events_url":"https://api.github.com/users/jimhester/events{/privacy}","received_events_url":"https://api.github.com/users/jimhester/received_events","type":"User","site_admin":false},"comments":5,"review_comments":0,"commits":6,"additions":91,"deletions":45,"changed_files":23}}