{"action":"opened","issue":{"url":"https://api.github.com/repos/ekg/vg/issues/93","labels_url":"https://api.github.com/repos/ekg/vg/issues/93/labels{/name}","comments_url":"https://api.github.com/repos/ekg/vg/issues/93/comments","events_url":"https://api.github.com/repos/ekg/vg/issues/93/events","html_url":"https://github.com/ekg/vg/issues/93","id":104271704,"number":93,"title":"travis failures","user":{"login":"ekg","id":145425,"avatar_url":"https://avatars.githubusercontent.com/u/145425?v=3","gravatar_id":"","url":"https://api.github.com/users/ekg","html_url":"https://github.com/ekg","followers_url":"https://api.github.com/users/ekg/followers","following_url":"https://api.github.com/users/ekg/following{/other_user}","gists_url":"https://api.github.com/users/ekg/gists{/gist_id}","starred_url":"https://api.github.com/users/ekg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ekg/subscriptions","organizations_url":"https://api.github.com/users/ekg/orgs","repos_url":"https://api.github.com/users/ekg/repos","events_url":"https://api.github.com/users/ekg/events{/privacy}","received_events_url":"https://api.github.com/users/ekg/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-09-01T13:52:57Z","updated_at":"2015-09-01T13:52:57Z","closed_at":null,"body":"Travis builds are still busted, specifically because of something happening in 07_vg_map.t:\r\n\r\n```text\r\nt/07_vg_map.t ........ \r\n1..15\r\nok 1 - global alignment traverses the correct path\r\nok 2 - alignment score is as expected\r\nok 3 - vg map takes -d as input without a variant graph\r\nok 4 - vg map can align across a SNP\r\nok 5 - alignment works on a small graph\r\nok 6 - binary alignment format is equivalent to json version\r\nok 7 - alignment from BAM correctly handles qualities\r\nok 8 - banded alignment produces a correct alignment\r\nok 9 - multiple alignments are returned in descending score order\r\nok 10 - mapping of BAM file produces expected number of alignments\r\nok 11 - mapping from a fastq produces the expected number of alignments\r\nnot ok 12 - vg connects paired-end reads in gam output\r\n#          got: '1666'\r\n#     expected: '1667'\r\nok 13 - mapping to graphs that can't be oriented without swapping edges works correctly\r\nok 14 - reads multi-map to multiple possible locations\r\nGCSA::prefixDoubling(): Initial path length 16\r\n  mergePaths(): 6404 -> 5987 paths\r\n  mergePaths(): 5937 unique, 50 unsorted, 0 nondeterministic paths\r\nGCSA::prefixDoubling(): Step 1 (path length 16 -> 32)\r\n  joinPaths(): 5987 -> 6091 paths (12336 ranks)\r\n  mergePaths(): 6091 -> 6091 paths\r\n  mergePaths(): 5937 unique, 0 unsorted, 154 nondeterministic paths\r\nGCSA::mergeByLabel(): 6091 -> 6014 paths\r\nGCSA::build(): 6507 edges\r\nGCSA::sample(): 1161 samples at 1084 positions\r\nok 15 - vg map works based on gcsa and xg indexes\r\nFailed 1/15 subtests \r\n```\r\n\r\nI dropped the previously-failing tests (unitig mapping ones) and it seemed to resolve this. Now, here we are again."}}