{"action":"created","issue":{"url":"https://api.github.com/repos/vgteam/vg/issues/405","repository_url":"https://api.github.com/repos/vgteam/vg","labels_url":"https://api.github.com/repos/vgteam/vg/issues/405/labels{/name}","comments_url":"https://api.github.com/repos/vgteam/vg/issues/405/comments","events_url":"https://api.github.com/repos/vgteam/vg/issues/405/events","html_url":"https://github.com/vgteam/vg/issues/405","id":162004514,"number":405,"title":"No alignments found when aligning with -a","user":{"login":"adamnovak","id":5062495,"avatar_url":"https://avatars.githubusercontent.com/u/5062495?v=3","gravatar_id":"","url":"https://api.github.com/users/adamnovak","html_url":"https://github.com/adamnovak","followers_url":"https://api.github.com/users/adamnovak/followers","following_url":"https://api.github.com/users/adamnovak/following{/other_user}","gists_url":"https://api.github.com/users/adamnovak/gists{/gist_id}","starred_url":"https://api.github.com/users/adamnovak/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/adamnovak/subscriptions","organizations_url":"https://api.github.com/users/adamnovak/orgs","repos_url":"https://api.github.com/users/adamnovak/repos","events_url":"https://api.github.com/users/adamnovak/events{/privacy}","received_events_url":"https://api.github.com/users/adamnovak/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2016-06-23T19:31:30Z","updated_at":"2016-06-24T18:16:33Z","closed_at":null,"body":"No alignments are found when aligning the NA12878 reads to this NA12878 BRCA2 graph. See the GAM and indexes in the attached file.\r\n\r\n[snp1kg-issue.tar.gz](https://github.com/vgteam/vg/files/330676/snp1kg-issue.tar.gz)\r\n\r\nSome of these reads ought to be consistent and survive the -a filter.\r\n\r\n`vg map -f NA12878.bam.fq -i -x graph.vg.xg -g graph.vg.gcsa -J | less` produces mapped alignments.\r\n\r\n`vg map -f NA12878.bam.fq -i -a -x graph.vg.xg -g graph.vg.gcsa -J | less` produces only unmapped alignments.\r\n"},"comment":{"url":"https://api.github.com/repos/vgteam/vg/issues/comments/228420371","html_url":"https://github.com/vgteam/vg/issues/405#issuecomment-228420371","issue_url":"https://api.github.com/repos/vgteam/vg/issues/405","id":228420371,"user":{"login":"glennhickey","id":901102,"avatar_url":"https://avatars.githubusercontent.com/u/901102?v=3","gravatar_id":"","url":"https://api.github.com/users/glennhickey","html_url":"https://github.com/glennhickey","followers_url":"https://api.github.com/users/glennhickey/followers","following_url":"https://api.github.com/users/glennhickey/following{/other_user}","gists_url":"https://api.github.com/users/glennhickey/gists{/gist_id}","starred_url":"https://api.github.com/users/glennhickey/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/glennhickey/subscriptions","organizations_url":"https://api.github.com/users/glennhickey/orgs","repos_url":"https://api.github.com/users/glennhickey/repos","events_url":"https://api.github.com/users/glennhickey/events{/privacy}","received_events_url":"https://api.github.com/users/glennhickey/received_events","type":"User","site_admin":false},"created_at":"2016-06-24T18:16:33Z","updated_at":"2016-06-24T18:16:33Z","body":"Something's still up.  While the alignments seem good now, only a handful\nhave mapping qualities (or at least non-zero mapping qualities).\n\nOn Thu, Jun 23, 2016 at 6:56 PM, jeizenga <notifications@github.com> wrote:\n\n> @ekg <https://github.com/ekg> Yeah, I think this is something that\n> happened when we were both working on paired end mapping at the same time.\n> I guess I didn't catch it before my last PR. The PR above fixes it though.\n>\n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/vgteam/vg/issues/405#issuecomment-228210327>, or mute\n> the thread\n> <https://github.com/notifications/unsubscribe/AA2_7nudM235LxJbTfaVhWOJq5TmxyY0ks5qOw86gaJpZM4I9KJ4>\n> .\n>\n"}}
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