GitHub PullRequestEvent at 2014-10-23 17:25:28
Repository: bcbio-nextgen
Actor: lpantano
Payload: {"action":"opened","number":649,"pull_request":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/pulls/649","id":23244406,"html_url":"https://github.com/chapmanb/bcbio-nextgen/pull/649","diff_url":"https://github.com/chapmanb/bcbio-nextgen/pull/649.diff","patch_url":"https://github.com/chapmanb/bcbio-nextgen/pull/649.patch","issue_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/649","number":649,"state":"open","locked":false,"title":"add script to merge FASTQ and BAM files","user":{"login":"lpantano","id":1621788,"avatar_url":"https://avatars.githubusercontent.com/u/1621788?v=2","gravatar_id":"","url":"https://api.github.com/users/lpantano","html_url":"https://github.com/lpantano","followers_url":"https://api.github.com/users/lpantano/followers","following_url":"https://api.github.com/users/lpantano/following{/other_user}","gists_url":"https://api.github.com/users/lpantano/gists{/gist_id}","starred_url":"https://api.github.com/users/lpantano/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lpantano/subscriptions","organizations_url":"https://api.github.com/users/lpantano/orgs","repos_url":"https://api.github.com/users/lpantano/repos","events_url":"https://api.github.com/users/lpantano/events{/privacy}","received_events_url":"https://api.github.com/users/lpantano/received_events","type":"User","site_admin":false},"body":"Hi,\r\n\r\nI tried to do it the best way to use bcbio functions and ipython cluster helper (I used some code I saw from  other project of @roryk). It is working in local and cluster, and with fastq and bam files.\r\n\r\nI add a function into `fastq.py` to merge: for now using `cat` (don't know if there is a better solution). As well, I had to modified `is_fastq` function to recognize `fastq.gz` (didn't work how it was, maybe you wanna look at that line). \r\n\r\nAs well, I modified `merge` inside `bam/__init__.py`. Some times the bam files are a mess ( like the ones I had it) and samtools will die with bad header or other errors. `bamtools`  seems to work with these cases, so I added that incase the other two tools fail. If you think I should do another function, happy to re-write code.\r\n\r\nAnd finally some documentation. Feel free to re-write any sentence that doesn't make sense.\r\n\r\n ","created_at":"2014-10-23T17:25:28Z","updated_at":"2014-10-23T17:25:28Z","closed_at":null,"merged_at":null,"merge_commit_sha":null,"assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/pulls/649/commits","review_comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/pulls/649/comments","review_comment_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/pulls/comments/{number}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/649/comments","statuses_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/statuses/8ac83b71b74a04ec0633a8b80da48a0e253b9c40","head":{"label":"lpantano:upstream","ref":"upstream","sha":"8ac83b71b74a04ec0633a8b80da48a0e253b9c40","user":{"login":"lpantano","id":1621788,"avatar_url":"https://avatars.githubusercontent.com/u/1621788?v=2","gravatar_id":"","url":"https://api.github.com/users/lpantano","html_url":"https://github.com/lpantano","followers_url":"https://api.github.com/users/lpantano/followers","following_url":"https://api.github.com/users/lpantano/following{/other_user}","gists_url":"https://api.github.com/users/lpantano/gists{/gist_id}","starred_url":"https://api.github.com/users/lpantano/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lpantano/subscriptions","organizations_url":"https://api.github.com/users/lpantano/orgs","repos_url":"https://api.github.com/users/lpantano/repos","events_url":"https://api.github.com/users/lpantano/events{/privacy}","received_events_url":"https://api.github.com/users/lpantano/received_events","type":"User","site_admin":false},"repo":{"id":20977788,"name":"bcbio-nextgen","full_name":"lpantano/bcbio-nextgen","owner":{"login":"lpantano","id":1621788,"avatar_url":"https://avatars.githubusercontent.com/u/1621788?v=2","gravatar_id":"","url":"https://api.github.com/users/lpantano","html_url":"https://github.com/lpantano","followers_url":"https://api.github.com/users/lpantano/followers","following_url":"https://api.github.com/users/lpantano/following{/other_user}","gists_url":"https://api.github.com/users/lpantano/gists{/gist_id}","starred_url":"https://api.github.com/users/lpantano/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lpantano/subscriptions","organizations_url":"https://api.github.com/users/lpantano/orgs","repos_url":"https://api.github.com/users/lpantano/repos","events_url":"https://api.github.com/users/lpantano/events{/privacy}","received_events_url":"https://api.github.com/users/lpantano/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/lpantano/bcbio-nextgen","description":"Validated, scalable, community developed variant calling and RNA-seq analysis","fork":true,"url":"https://api.github.com/repos/lpantano/bcbio-nextgen","forks_url":"https://api.github.com/repos/lpantano/bcbio-nextgen/forks","keys_url":"https://api.github.com/repos/lpantano/bcbio-nextgen/keys{/key_id}","collaborators_url":"https://api.github.com/repos/lpantano/bcbio-nextgen/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/lpantano/bcbio-nextgen/teams","hooks_url":"https://api.github.com/repos/lpantano/bcbio-nextgen/hooks","issue_events_url":"https://api.github.com/repos/lpantano/bcbio-nextgen/issues/events{/number}","events_url":"https://api.github.com/repos/lpantano/bcbio-nextgen/events","assignees_url":"https://api.github.com/repos/lpantano/bcbio-nextgen/assignees{/user}","branches_url":"https://api.github.com/repos/lpantano/bcbio-nextgen/branches{/branch}","tags_url":"https://api.github.com/repos/lpantano/bcbio-nextgen/tags","blobs_url":"https://api.github.com/repos/lpantano/bcbio-nextgen/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/lpantano/bcbio-nextgen/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/lpantano/bcbio-nextgen/git/refs{/sha}","trees_url":"https://api.github.com/repos/lpantano/bcbio-nextgen/git/trees{/sha}","statuses_url":"https://api.github.com/repos/lpantano/bcbio-nextgen/statuses/{sha}","languages_url":"https://api.github.com/repos/lpantano/bcbio-nextgen/languages","stargazers_url":"https://api.github.com/repos/lpantano/bcbio-nextgen/stargazers","contributors_url":"https://api.github.com/repos/lpantano/bcbio-nextgen/contributors","subscribers_url":"https://api.github.com/repos/lpantano/bcbio-nextgen/subscribers","subscription_url":"https://api.github.com/repos/lpantano/bcbio-nextgen/subscription","commits_url":"https://api.github.com/repos/lpantano/bcbio-nextgen/commits{/sha}","git_commits_url":"https://api.github.com/repos/lpantano/bcbio-nextgen/git/commits{/sha}","comments_url":"https://api.github.com/repos/lpantano/bcbio-nextgen/comments{/number}","issue_comment_url":"https://api.github.com/repos/lpantano/bcbio-nextgen/issues/comments/{number}","contents_url":"https://api.github.com/repos/lpantano/bcbio-nextgen/contents/{+path}","compare_url":"https://api.github.com/repos/lpantano/bcbio-nextgen/compare/{base}...{head}","merges_url":"https://api.github.com/repos/lpantano/bcbio-nextgen/merges","archive_url":"https://api.github.com/repos/lpantano/bcbio-nextgen/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/lpantano/bcbio-nextgen/downloads","issues_url":"https://api.github.com/repos/lpantano/bcbio-nextgen/issues{/number}","pulls_url":"https://api.github.com/repos/lpantano/bcbio-nextgen/pulls{/number}","milestones_url":"https://api.github.com/repos/lpantano/bcbio-nextgen/milestones{/number}","notifications_url":"https://api.github.com/repos/lpantano/bcbio-nextgen/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/lpantano/bcbio-nextgen/labels{/name}","releases_url":"https://api.github.com/repos/lpantano/bcbio-nextgen/releases{/id}","created_at":"2014-06-18T20:59:21Z","updated_at":"2014-09-04T15:35:59Z","pushed_at":"2014-10-23T17:14:43Z","git_url":"git://github.com/lpantano/bcbio-nextgen.git","ssh_url":"git@github.com:lpantano/bcbio-nextgen.git","clone_url":"https://github.com/lpantano/bcbio-nextgen.git","svn_url":"https://github.com/lpantano/bcbio-nextgen","homepage":"https://bcbio-nextgen.readthedocs.org","size":18168,"stargazers_count":1,"watchers_count":1,"language":"Python","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":1,"default_branch":"master"}},"base":{"label":"chapmanb:master","ref":"master","sha":"30516c1e6165e1eb48a9d3b2df0481985836d7c8","user":{"login":"chapmanb","id":39391,"avatar_url":"https://avatars.githubusercontent.com/u/39391?v=2","gravatar_id":"","url":"https://api.github.com/users/chapmanb","html_url":"https://github.com/chapmanb","followers_url":"https://api.github.com/users/chapmanb/followers","following_url":"https://api.github.com/users/chapmanb/following{/other_user}","gists_url":"https://api.github.com/users/chapmanb/gists{/gist_id}","starred_url":"https://api.github.com/users/chapmanb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chapmanb/subscriptions","organizations_url":"https://api.github.com/users/chapmanb/orgs","repos_url":"https://api.github.com/users/chapmanb/repos","events_url":"https://api.github.com/users/chapmanb/events{/privacy}","received_events_url":"https://api.github.com/users/chapmanb/received_events","type":"User","site_admin":false},"repo":{"id":8049897,"name":"bcbio-nextgen","full_name":"chapmanb/bcbio-nextgen","owner":{"login":"chapmanb","id":39391,"avatar_url":"https://avatars.githubusercontent.com/u/39391?v=2","gravatar_id":"","url":"https://api.github.com/users/chapmanb","html_url":"https://github.com/chapmanb","followers_url":"https://api.github.com/users/chapmanb/followers","following_url":"https://api.github.com/users/chapmanb/following{/other_user}","gists_url":"https://api.github.com/users/chapmanb/gists{/gist_id}","starred_url":"https://api.github.com/users/chapmanb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chapmanb/subscriptions","organizations_url":"https://api.github.com/users/chapmanb/orgs","repos_url":"https://api.github.com/users/chapmanb/repos","events_url":"https://api.github.com/users/chapmanb/events{/privacy}","received_events_url":"https://api.github.com/users/chapmanb/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/chapmanb/bcbio-nextgen","description":"Validated, scalable, community developed variant calling and RNA-seq analysis","fork":false,"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen","forks_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/forks","keys_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/keys{/key_id}","collaborators_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/teams","hooks_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/hooks","issue_events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/events{/number}","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/events","assignees_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/assignees{/user}","branches_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/branches{/branch}","tags_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/tags","blobs_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/git/refs{/sha}","trees_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/git/trees{/sha}","statuses_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/statuses/{sha}","languages_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/languages","stargazers_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/stargazers","contributors_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/contributors","subscribers_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/subscribers","subscription_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/subscription","commits_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/commits{/sha}","git_commits_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/git/commits{/sha}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/comments{/number}","issue_comment_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/comments/{number}","contents_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/contents/{+path}","compare_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/compare/{base}...{head}","merges_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/merges","archive_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/downloads","issues_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues{/number}","pulls_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/pulls{/number}","milestones_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/milestones{/number}","notifications_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/labels{/name}","releases_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/releases{/id}","created_at":"2013-02-06T11:14:50Z","updated_at":"2014-10-20T19:00:07Z","pushed_at":"2014-10-23T15:39:45Z","git_url":"git://github.com/chapmanb/bcbio-nextgen.git","ssh_url":"git@github.com:chapmanb/bcbio-nextgen.git","clone_url":"https://github.com/chapmanb/bcbio-nextgen.git","svn_url":"https://github.com/chapmanb/bcbio-nextgen","homepage":"https://bcbio-nextgen.readthedocs.org","size":28718,"stargazers_count":145,"watchers_count":145,"language":"Python","has_issues":true,"has_downloads":true,"has_wiki":false,"has_pages":false,"forks_count":72,"mirror_url":null,"open_issues_count":34,"forks":72,"open_issues":34,"watchers":145,"default_branch":"master"}},"_links":{"self":{"href":"https://api.github.com/repos/chapmanb/bcbio-nextgen/pulls/649"},"html":{"href":"https://github.com/chapmanb/bcbio-nextgen/pull/649"},"issue":{"href":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/649"},"comments":{"href":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/649/comments"},"review_comments":{"href":"https://api.github.com/repos/chapmanb/bcbio-nextgen/pulls/649/comments"},"review_comment":{"href":"https://api.github.com/repos/chapmanb/bcbio-nextgen/pulls/comments/{number}"},"commits":{"href":"https://api.github.com/repos/chapmanb/bcbio-nextgen/pulls/649/commits"},"statuses":{"href":"https://api.github.com/repos/chapmanb/bcbio-nextgen/statuses/8ac83b71b74a04ec0633a8b80da48a0e253b9c40"}},"merged":false,"mergeable":null,"mergeable_state":"unknown","merged_by":null,"comments":0,"review_comments":0,"commits":3,"additions":188,"deletions":7,"changed_files":4}}