{"action":"created","issue":{"url":"https://api.github.com/repos/eturro/mmseq/issues/13","repository_url":"https://api.github.com/repos/eturro/mmseq","labels_url":"https://api.github.com/repos/eturro/mmseq/issues/13/labels{/name}","comments_url":"https://api.github.com/repos/eturro/mmseq/issues/13/comments","events_url":"https://api.github.com/repos/eturro/mmseq/issues/13/events","html_url":"https://github.com/eturro/mmseq/issues/13","id":155103225,"number":13,"title":"how to supply regex for bam2hits with single sequence name?","user":{"login":"n-long","id":8417928,"avatar_url":"https://avatars.githubusercontent.com/u/8417928?v=3","gravatar_id":"","url":"https://api.github.com/users/n-long","html_url":"https://github.com/n-long","followers_url":"https://api.github.com/users/n-long/followers","following_url":"https://api.github.com/users/n-long/following{/other_user}","gists_url":"https://api.github.com/users/n-long/gists{/gist_id}","starred_url":"https://api.github.com/users/n-long/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/n-long/subscriptions","organizations_url":"https://api.github.com/users/n-long/orgs","repos_url":"https://api.github.com/users/n-long/repos","events_url":"https://api.github.com/users/n-long/events{/privacy}","received_events_url":"https://api.github.com/users/n-long/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2016-05-16T19:32:15Z","updated_at":"2016-05-17T03:47:10Z","closed_at":null,"body":"Hello,\r\n\r\nAll of my sequence headers share a single word format such as GENE_strain. I added a gene and transcript identifier originally, but my read mapping failed when using '--fullref' argument to bowtie1 using tophat (you can add all of the arguments at around line 2349 in the tophat executable). I had to go that route since using bowtie as provided in the manual was not producing a proper SAM alignment format, despite correct flags. Anyway, all my gene and transcript identifiers are 1:1 anyway, but I cannot figure out the regex pattern to make bam2hits assign the sequence header to both identifiers.\r\n\r\nI've gotten this far but I can't get past a segfault. \r\nbam2hits -m \\\"(\\S+)\\\" 1 1\r\n\r\nThanks.\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/eturro/mmseq/issues/comments/219612509","html_url":"https://github.com/eturro/mmseq/issues/13#issuecomment-219612509","issue_url":"https://api.github.com/repos/eturro/mmseq/issues/13","id":219612509,"user":{"login":"n-long","id":8417928,"avatar_url":"https://avatars.githubusercontent.com/u/8417928?v=3","gravatar_id":"","url":"https://api.github.com/users/n-long","html_url":"https://github.com/n-long","followers_url":"https://api.github.com/users/n-long/followers","following_url":"https://api.github.com/users/n-long/following{/other_user}","gists_url":"https://api.github.com/users/n-long/gists{/gist_id}","starred_url":"https://api.github.com/users/n-long/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/n-long/subscriptions","organizations_url":"https://api.github.com/users/n-long/orgs","repos_url":"https://api.github.com/users/n-long/repos","events_url":"https://api.github.com/users/n-long/events{/privacy}","received_events_url":"https://api.github.com/users/n-long/received_events","type":"User","site_admin":false},"created_at":"2016-05-17T03:47:10Z","updated_at":"2016-05-17T03:47:10Z","body":"Interestingly, the same bowtie command works on the raw fastq sequence files if I do not include the '--fullref' option\r\n\r\nhere are the sequence headers for my transcript reference\r\n\r\n`>TC002292_des\tgene:TC002292_des\ttranscript:TC002292_des\r\n>TC002291_des\tgene:TC002291_des\ttranscript:TC002291_des\r\n>TC002290_des\tgene:TC002290_des\ttranscript:TC002290_des\r\n>TC002293_des\tgene:TC002293_des\ttranscript:TC002293_des\r\n>TC002289_des\tgene:TC002289_des\ttranscript:TC002289_des\r\n>TC002294_des\tgene:TC002294_des\ttranscript:TC002294_des\r\n>TC002288_des\tgene:TC002288_des\ttranscript:TC002288_des\r\n>TC002287_des\tgene:TC002287_des\ttranscript:TC002287_des\r\n>TC002286_des\tgene:TC002286_des\ttranscript:TC002286_des\r\n>TC002285_des\tgene:TC002285_des\ttranscript:TC002285_des`"}}