{"action":"created","comment":{"url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/pulls/comments/45923531","id":45923531,"diff_hunk":"@@ -683,16 +679,14 @@ size_t Recursor::FillAlphaBeta(M& a, M& b) const throw(AlphaBetaMismatch)\n             FillBeta(a, b);\n \n         ++flipflops;\n-        // std::cout << \"Alpha Used: \" << a.UsedEntries() << \"  Beta Used:  \" << b.UsedEntries() <<\n-        // std::endl;\n     }\n \n     if (std::abs(1.0 - alphaV / betaV) > ALPHA_BETA_MISMATCH_TOLERANCE) {\n-        // LDEBUG << \"Could not mate alpha, beta.  Read: \" << read_.Name << \"\n-        // Tpl: Was wrapped, improve debugging to pring\";\n-        // std::cout << \"Mismatch : \" << mismatch_percentage << \"% Alpha \" <<\n-        // alphaV << \" Beta \" << betaV << std::endl;\n-        throw AlphaBetaMismatch();\n+        // try at least one time to break out of this by increasing banding","path":"src/Recursor.cpp","position":53,"original_position":53,"commit_id":"9ce71bd12ee0f3054bc7f7ba8eab155fadee616d","original_commit_id":"9ce71bd12ee0f3054bc7f7ba8eab155fadee616d","user":{"login":"evolvedmicrobe","id":1330626,"avatar_url":"https://avatars.githubusercontent.com/u/1330626?v=3","gravatar_id":"","url":"https://api.github.com/users/evolvedmicrobe","html_url":"https://github.com/evolvedmicrobe","followers_url":"https://api.github.com/users/evolvedmicrobe/followers","following_url":"https://api.github.com/users/evolvedmicrobe/following{/other_user}","gists_url":"https://api.github.com/users/evolvedmicrobe/gists{/gist_id}","starred_url":"https://api.github.com/users/evolvedmicrobe/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/evolvedmicrobe/subscriptions","organizations_url":"https://api.github.com/users/evolvedmicrobe/orgs","repos_url":"https://api.github.com/users/evolvedmicrobe/repos","events_url":"https://api.github.com/users/evolvedmicrobe/events{/privacy}","received_events_url":"https://api.github.com/users/evolvedmicrobe/received_events","type":"User","site_admin":false},"body":"This likely needs a unit test.","created_at":"2015-11-25T21:54:49Z","updated_at":"2015-11-25T21:54:49Z","html_url":"https://github.com/PacificBiosciences/ConsensusCore2/pull/7#discussion_r45923531","pull_request_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/pulls/7","_links":{"self":{"href":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/pulls/comments/45923531"},"html":{"href":"https://github.com/PacificBiosciences/ConsensusCore2/pull/7#discussion_r45923531"},"pull_request":{"href":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/pulls/7"}}},"pull_request":{"url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/pulls/7","id":51843321,"html_url":"https://github.com/PacificBiosciences/ConsensusCore2/pull/7","diff_url":"https://github.com/PacificBiosciences/ConsensusCore2/pull/7.diff","patch_url":"https://github.com/PacificBiosciences/ConsensusCore2/pull/7.patch","issue_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/issues/7","number":7,"state":"open","locked":false,"title":"Retry once in case of AlphaBetaMismatch","user":{"login":"nlhepler","id":38372,"avatar_url":"https://avatars.githubusercontent.com/u/38372?v=3","gravatar_id":"","url":"https://api.github.com/users/nlhepler","html_url":"https://github.com/nlhepler","followers_url":"https://api.github.com/users/nlhepler/followers","following_url":"https://api.github.com/users/nlhepler/following{/other_user}","gists_url":"https://api.github.com/users/nlhepler/gists{/gist_id}","starred_url":"https://api.github.com/users/nlhepler/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nlhepler/subscriptions","organizations_url":"https://api.github.com/users/nlhepler/orgs","repos_url":"https://api.github.com/users/nlhepler/repos","events_url":"https://api.github.com/users/nlhepler/events{/privacy}","received_events_url":"https://api.github.com/users/nlhepler/received_events","type":"User","site_admin":false},"body":"When detecting an AlphaBetaMismatch, retry once after doubling scoreDiff_","created_at":"2015-11-25T20:36:45Z","updated_at":"2015-11-25T21:54:49Z","closed_at":null,"merged_at":null,"merge_commit_sha":"0201cc0419ae62a0c16bee7ccbb5520e33d47721","assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/pulls/7/commits","review_comments_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/pulls/7/comments","review_comment_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/pulls/comments{/number}","comments_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/issues/7/comments","statuses_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/statuses/9ce71bd12ee0f3054bc7f7ba8eab155fadee616d","head":{"label":"PacificBiosciences:retryFill","ref":"retryFill","sha":"9ce71bd12ee0f3054bc7f7ba8eab155fadee616d","user":{"login":"PacificBiosciences","id":999745,"avatar_url":"https://avatars.githubusercontent.com/u/999745?v=3","gravatar_id":"","url":"https://api.github.com/users/PacificBiosciences","html_url":"https://github.com/PacificBiosciences","followers_url":"https://api.github.com/users/PacificBiosciences/followers","following_url":"https://api.github.com/users/PacificBiosciences/following{/other_user}","gists_url":"https://api.github.com/users/PacificBiosciences/gists{/gist_id}","starred_url":"https://api.github.com/users/PacificBiosciences/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/PacificBiosciences/subscriptions","organizations_url":"https://api.github.com/users/PacificBiosciences/orgs","repos_url":"https://api.github.com/users/PacificBiosciences/repos","events_url":"https://api.github.com/users/PacificBiosciences/events{/privacy}","received_events_url":"https://api.github.com/users/PacificBiosciences/received_events","type":"Organization","site_admin":false},"repo":{"id":44767613,"name":"ConsensusCore2","full_name":"PacificBiosciences/ConsensusCore2","owner":{"login":"PacificBiosciences","id":999745,"avatar_url":"https://avatars.githubusercontent.com/u/999745?v=3","gravatar_id":"","url":"https://api.github.com/users/PacificBiosciences","html_url":"https://github.com/PacificBiosciences","followers_url":"https://api.github.com/users/PacificBiosciences/followers","following_url":"https://api.github.com/users/PacificBiosciences/following{/other_user}","gists_url":"https://api.github.com/users/PacificBiosciences/gists{/gist_id}","starred_url":"https://api.github.com/users/PacificBiosciences/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/PacificBiosciences/subscriptions","organizations_url":"https://api.github.com/users/PacificBiosciences/orgs","repos_url":"https://api.github.com/users/PacificBiosciences/repos","events_url":"https://api.github.com/users/PacificBiosciences/events{/privacy}","received_events_url":"https://api.github.com/users/PacificBiosciences/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/PacificBiosciences/ConsensusCore2","description":"PacBio consensus routines with SWIG bindings (Arrow model--successor to Quiver)","fork":false,"url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2","forks_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/forks","keys_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/keys{/key_id}","collaborators_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/teams","hooks_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/hooks","issue_events_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/issues/events{/number}","events_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/events","assignees_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/assignees{/user}","branches_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/branches{/branch}","tags_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/tags","blobs_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/git/refs{/sha}","trees_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/git/trees{/sha}","statuses_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/statuses/{sha}","languages_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/languages","stargazers_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/stargazers","contributors_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/contributors","subscribers_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/subscribers","subscription_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/subscription","commits_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/commits{/sha}","git_commits_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/git/commits{/sha}","comments_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/comments{/number}","issue_comment_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/issues/comments{/number}","contents_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/contents/{+path}","compare_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/compare/{base}...{head}","merges_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/merges","archive_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/downloads","issues_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/issues{/number}","pulls_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/pulls{/number}","milestones_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/milestones{/number}","notifications_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/labels{/name}","releases_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/releases{/id}","created_at":"2015-10-22T19:14:48Z","updated_at":"2015-10-23T17:31:54Z","pushed_at":"2015-11-25T20:36:46Z","git_url":"git://github.com/PacificBiosciences/ConsensusCore2.git","ssh_url":"git@github.com:PacificBiosciences/ConsensusCore2.git","clone_url":"https://github.com/PacificBiosciences/ConsensusCore2.git","svn_url":"https://github.com/PacificBiosciences/ConsensusCore2","homepage":"","size":554,"stargazers_count":0,"watchers_count":0,"language":"C++","has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":0,"mirror_url":null,"open_issues_count":2,"forks":0,"open_issues":2,"watchers":0,"default_branch":"master"}},"base":{"label":"PacificBiosciences:master","ref":"master","sha":"7e483b87155c8514655bb5e82ff92c3cafb870ce","user":{"login":"PacificBiosciences","id":999745,"avatar_url":"https://avatars.githubusercontent.com/u/999745?v=3","gravatar_id":"","url":"https://api.github.com/users/PacificBiosciences","html_url":"https://github.com/PacificBiosciences","followers_url":"https://api.github.com/users/PacificBiosciences/followers","following_url":"https://api.github.com/users/PacificBiosciences/following{/other_user}","gists_url":"https://api.github.com/users/PacificBiosciences/gists{/gist_id}","starred_url":"https://api.github.com/users/PacificBiosciences/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/PacificBiosciences/subscriptions","organizations_url":"https://api.github.com/users/PacificBiosciences/orgs","repos_url":"https://api.github.com/users/PacificBiosciences/repos","events_url":"https://api.github.com/users/PacificBiosciences/events{/privacy}","received_events_url":"https://api.github.com/users/PacificBiosciences/received_events","type":"Organization","site_admin":false},"repo":{"id":44767613,"name":"ConsensusCore2","full_name":"PacificBiosciences/ConsensusCore2","owner":{"login":"PacificBiosciences","id":999745,"avatar_url":"https://avatars.githubusercontent.com/u/999745?v=3","gravatar_id":"","url":"https://api.github.com/users/PacificBiosciences","html_url":"https://github.com/PacificBiosciences","followers_url":"https://api.github.com/users/PacificBiosciences/followers","following_url":"https://api.github.com/users/PacificBiosciences/following{/other_user}","gists_url":"https://api.github.com/users/PacificBiosciences/gists{/gist_id}","starred_url":"https://api.github.com/users/PacificBiosciences/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/PacificBiosciences/subscriptions","organizations_url":"https://api.github.com/users/PacificBiosciences/orgs","repos_url":"https://api.github.com/users/PacificBiosciences/repos","events_url":"https://api.github.com/users/PacificBiosciences/events{/privacy}","received_events_url":"https://api.github.com/users/PacificBiosciences/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/PacificBiosciences/ConsensusCore2","description":"PacBio consensus routines with SWIG bindings (Arrow model--successor to Quiver)","fork":false,"url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2","forks_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/forks","keys_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/keys{/key_id}","collaborators_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/teams","hooks_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/hooks","issue_events_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/issues/events{/number}","events_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/events","assignees_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/assignees{/user}","branches_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/branches{/branch}","tags_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/tags","blobs_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/git/refs{/sha}","trees_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/git/trees{/sha}","statuses_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/statuses/{sha}","languages_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/languages","stargazers_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/stargazers","contributors_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/contributors","subscribers_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/subscribers","subscription_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/subscription","commits_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/commits{/sha}","git_commits_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/git/commits{/sha}","comments_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/comments{/number}","issue_comment_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/issues/comments{/number}","contents_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/contents/{+path}","compare_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/compare/{base}...{head}","merges_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/merges","archive_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/downloads","issues_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/issues{/number}","pulls_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/pulls{/number}","milestones_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/milestones{/number}","notifications_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/labels{/name}","releases_url":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/releases{/id}","created_at":"2015-10-22T19:14:48Z","updated_at":"2015-10-23T17:31:54Z","pushed_at":"2015-11-25T20:36:46Z","git_url":"git://github.com/PacificBiosciences/ConsensusCore2.git","ssh_url":"git@github.com:PacificBiosciences/ConsensusCore2.git","clone_url":"https://github.com/PacificBiosciences/ConsensusCore2.git","svn_url":"https://github.com/PacificBiosciences/ConsensusCore2","homepage":"","size":554,"stargazers_count":0,"watchers_count":0,"language":"C++","has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":0,"mirror_url":null,"open_issues_count":2,"forks":0,"open_issues":2,"watchers":0,"default_branch":"master"}},"_links":{"self":{"href":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/pulls/7"},"html":{"href":"https://github.com/PacificBiosciences/ConsensusCore2/pull/7"},"issue":{"href":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/issues/7"},"comments":{"href":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/issues/7/comments"},"review_comments":{"href":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/pulls/7/comments"},"review_comment":{"href":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/pulls/7/commits"},"statuses":{"href":"https://api.github.com/repos/PacificBiosciences/ConsensusCore2/statuses/9ce71bd12ee0f3054bc7f7ba8eab155fadee616d"}}}}