{"action":"created","comment":{"url":"https://api.github.com/repos/genome/genome/pulls/comments/31666275","id":31666275,"diff_hunk":"@@ -13,13 +13,82 @@ class Genome::InstrumentData::AlignmentResult::Speedseq {\n     ],\n };\n \n-sub _run_aligner {\n+sub post_create {\n+    return 1;\n+}\n+\n+sub get_bam_file {\n+    my $self = shift;\n+\n+    # Create doesn't do all of the necessary post-processing. This is being\n+    # delayed until the first time that the bam file is revivified.\n+    # If we don't have an allocation then this is the first revivification and\n+    # we will need to do post-processing.\n+    my $guard = $self->get_speedseq_bam_lock->unlock_guard();\n+    unless ($self->disk_allocations) {\n+        return $self->_inititalize_revivified_bam;\n+    }\n+    else {\n+        return $self->SUPER::get_bam_file;\n+    }\n+}\n+\n+sub get_speedseq_bam_lock {","path":"lib/perl/Genome/InstrumentData/AlignmentResult/Speedseq.pm","position":25,"original_position":25,"commit_id":"bc5fd00deaea5e9f68a9c51d7a2e3ace78b07792","original_commit_id":"bc5fd00deaea5e9f68a9c51d7a2e3ace78b07792","user":{"login":"brummett","id":111808,"avatar_url":"https://avatars.githubusercontent.com/u/111808?v=3","gravatar_id":"","url":"https://api.github.com/users/brummett","html_url":"https://github.com/brummett","followers_url":"https://api.github.com/users/brummett/followers","following_url":"https://api.github.com/users/brummett/following{/other_user}","gists_url":"https://api.github.com/users/brummett/gists{/gist_id}","starred_url":"https://api.github.com/users/brummett/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/brummett/subscriptions","organizations_url":"https://api.github.com/users/brummett/orgs","repos_url":"https://api.github.com/users/brummett/repos","events_url":"https://api.github.com/users/brummett/events{/privacy}","received_events_url":"https://api.github.com/users/brummett/received_events","type":"User","site_admin":false},"body":"Would ```$self->class``` replace ```__PACKAGE__```?","created_at":"2015-06-03T20:29:21Z","updated_at":"2015-06-03T20:29:21Z","html_url":"https://github.com/genome/genome/pull/796#discussion_r31666275","pull_request_url":"https://api.github.com/repos/genome/genome/pulls/796","_links":{"self":{"href":"https://api.github.com/repos/genome/genome/pulls/comments/31666275"},"html":{"href":"https://github.com/genome/genome/pull/796#discussion_r31666275"},"pull_request":{"href":"https://api.github.com/repos/genome/genome/pulls/796"}}},"pull_request":{"url":"https://api.github.com/repos/genome/genome/pulls/796","id":36853359,"html_url":"https://github.com/genome/genome/pull/796","diff_url":"https://github.com/genome/genome/pull/796.diff","patch_url":"https://github.com/genome/genome/pull/796.patch","issue_url":"https://api.github.com/repos/genome/genome/issues/796","number":796,"state":"open","locked":false,"title":"AlignAndMerge only creates per-lane alignment objects without revivification","user":{"login":"susannasiebert","id":6617192,"avatar_url":"https://avatars.githubusercontent.com/u/6617192?v=3","gravatar_id":"","url":"https://api.github.com/users/susannasiebert","html_url":"https://github.com/susannasiebert","followers_url":"https://api.github.com/users/susannasiebert/followers","following_url":"https://api.github.com/users/susannasiebert/following{/other_user}","gists_url":"https://api.github.com/users/susannasiebert/gists{/gist_id}","starred_url":"https://api.github.com/users/susannasiebert/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/susannasiebert/subscriptions","organizations_url":"https://api.github.com/users/susannasiebert/orgs","repos_url":"https://api.github.com/users/susannasiebert/repos","events_url":"https://api.github.com/users/susannasiebert/events{/privacy}","received_events_url":"https://api.github.com/users/susannasiebert/received_events","type":"User","site_admin":false},"body":"Previously the AlignAndMerge step would create a merged alignment object (e.g. run Speedseq) and then use it to create the per-lane alignment objects. We would use revivification to create the per-lane bam so that we could create a .header and .flagstat file (and do some other per-lane alignment processing). As a result of having to revivifiy each per-lane bam for all the instrument data (in serial), the AlignAndMerge step would run extremely long.\r\n\r\nThis PR makes it so that the AlignAndMerge step will still run the aligner to create the merged alignment object but this step will only create the per-lane alignment objects without any further processing. .header and .flagstat file creation are postponed until the first call to get_bam_file. Calling this subroutine will run revivification anyway and we then do all the necessary post-processing at this point.","created_at":"2015-06-03T16:49:59Z","updated_at":"2015-06-03T20:29:21Z","closed_at":null,"merged_at":null,"merge_commit_sha":"ace59256c4e34c51641c285bab99f1840a4da171","assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/genome/genome/pulls/796/commits","review_comments_url":"https://api.github.com/repos/genome/genome/pulls/796/comments","review_comment_url":"https://api.github.com/repos/genome/genome/pulls/comments{/number}","comments_url":"https://api.github.com/repos/genome/genome/issues/796/comments","statuses_url":"https://api.github.com/repos/genome/genome/statuses/bc5fd00deaea5e9f68a9c51d7a2e3ace78b07792","head":{"label":"susannasiebert:speedseq_improvements","ref":"speedseq_improvements","sha":"bc5fd00deaea5e9f68a9c51d7a2e3ace78b07792","user":{"login":"susannasiebert","id":6617192,"avatar_url":"https://avatars.githubusercontent.com/u/6617192?v=3","gravatar_id":"","url":"https://api.github.com/users/susannasiebert","html_url":"https://github.com/susannasiebert","followers_url":"https://api.github.com/users/susannasiebert/followers","following_url":"https://api.github.com/users/susannasiebert/following{/other_user}","gists_url":"https://api.github.com/users/susannasiebert/gists{/gist_id}","starred_url":"https://api.github.com/users/susannasiebert/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/susannasiebert/subscriptions","organizations_url":"https://api.github.com/users/susannasiebert/orgs","repos_url":"https://api.github.com/users/susannasiebert/repos","events_url":"https://api.github.com/users/susannasiebert/events{/privacy}","received_events_url":"https://api.github.com/users/susannasiebert/received_events","type":"User","site_admin":false},"repo":{"id":23836901,"name":"genome","full_name":"susannasiebert/genome","owner":{"login":"susannasiebert","id":6617192,"avatar_url":"https://avatars.githubusercontent.com/u/6617192?v=3","gravatar_id":"","url":"https://api.github.com/users/susannasiebert","html_url":"https://github.com/susannasiebert","followers_url":"https://api.github.com/users/susannasiebert/followers","following_url":"https://api.github.com/users/susannasiebert/following{/other_user}","gists_url":"https://api.github.com/users/susannasiebert/gists{/gist_id}","starred_url":"https://api.github.com/users/susannasiebert/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/susannasiebert/subscriptions","organizations_url":"https://api.github.com/users/susannasiebert/orgs","repos_url":"https://api.github.com/users/susannasiebert/repos","events_url":"https://api.github.com/users/susannasiebert/events{/privacy}","received_events_url":"https://api.github.com/users/susannasiebert/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/susannasiebert/genome","description":"","fork":true,"url":"https://api.github.com/repos/susannasiebert/genome","forks_url":"https://api.github.com/repos/susannasiebert/genome/forks","keys_url":"https://api.github.com/repos/susannasiebert/genome/keys{/key_id}","collaborators_url":"https://api.github.com/repos/susannasiebert/genome/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/susannasiebert/genome/teams","hooks_url":"https://api.github.com/repos/susannasiebert/genome/hooks","issue_events_url":"https://api.github.com/repos/susannasiebert/genome/issues/events{/number}","events_url":"https://api.github.com/repos/susannasiebert/genome/events","assignees_url":"https://api.github.com/repos/susannasiebert/genome/assignees{/user}","branches_url":"https://api.github.com/repos/susannasiebert/genome/branches{/branch}","tags_url":"https://api.github.com/repos/susannasiebert/genome/tags","blobs_url":"https://api.github.com/repos/susannasiebert/genome/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/susannasiebert/genome/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/susannasiebert/genome/git/refs{/sha}","trees_url":"https://api.github.com/repos/susannasiebert/genome/git/trees{/sha}","statuses_url":"https://api.github.com/repos/susannasiebert/genome/statuses/{sha}","languages_url":"https://api.github.com/repos/susannasiebert/genome/languages","stargazers_url":"https://api.github.com/repos/susannasiebert/genome/stargazers","contributors_url":"https://api.github.com/repos/susannasiebert/genome/contributors","subscribers_url":"https://api.github.com/repos/susannasiebert/genome/subscribers","subscription_url":"https://api.github.com/repos/susannasiebert/genome/subscription","commits_url":"https://api.github.com/repos/susannasiebert/genome/commits{/sha}","git_commits_url":"https://api.github.com/repos/susannasiebert/genome/git/commits{/sha}","comments_url":"https://api.github.com/repos/susannasiebert/genome/comments{/number}","issue_comment_url":"https://api.github.com/repos/susannasiebert/genome/issues/comments{/number}","contents_url":"https://api.github.com/repos/susannasiebert/genome/contents/{+path}","compare_url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