{"action":"created","issue":{"url":"https://api.github.com/repos/night-stalker/ERIF/issues/2","labels_url":"https://api.github.com/repos/night-stalker/ERIF/issues/2/labels{/name}","comments_url":"https://api.github.com/repos/night-stalker/ERIF/issues/2/comments","events_url":"https://api.github.com/repos/night-stalker/ERIF/issues/2/events","html_url":"https://github.com/night-stalker/ERIF/issues/2","id":101673671,"number":2,"title":" test_reads.sam_ext.txt  not created","user":{"login":"averagehat","id":5606168,"avatar_url":"https://avatars.githubusercontent.com/u/5606168?v=3","gravatar_id":"","url":"https://api.github.com/users/averagehat","html_url":"https://github.com/averagehat","followers_url":"https://api.github.com/users/averagehat/followers","following_url":"https://api.github.com/users/averagehat/following{/other_user}","gists_url":"https://api.github.com/users/averagehat/gists{/gist_id}","starred_url":"https://api.github.com/users/averagehat/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/averagehat/subscriptions","organizations_url":"https://api.github.com/users/averagehat/orgs","repos_url":"https://api.github.com/users/averagehat/repos","events_url":"https://api.github.com/users/averagehat/events{/privacy}","received_events_url":"https://api.github.com/users/averagehat/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-08-18T14:45:21Z","updated_at":"2015-08-28T21:12:05Z","closed_at":null,"body":"Using the data under \"__Example__\" [here](http://alan.cs.gsu.edu/NGS/?q=content/kgem):\r\n\r\n```\r\nbash-4.1$ java -jar ../ERIF-1.0.jar -g reference.fa -i sample_data.fa -o test_\r\n00:00:07 Mapped: 19999          Unmapped: 0             Too small: 0            Pre align: 20000                In align: 19999         Post align: 20000      \r\n\r\nSubstitution matrix:\r\nr/g\tA\tC\tG\tT\t-\tN\r\nA\t0.17843\t0.00631\t0.00767\t0.00608\t2.91E-4\t0.0\r\nC\t0.00329\t0.26067\t0.00622\t0.00615\t5.00E-4\t0.0\r\nG\t0.00209\t0.00442\t0.29542\t0.00497\t0.00114\t0.0\r\nT\t0.00191\t0.00190\t0.00265\t0.20747\t2.11E-4\t0.0\r\n-\t1.12E-4\t5.74E-4\t0.00111\t3.42E-4\t0.0\t0.0\r\nN\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\r\nSUBSTITUTIONS: 0.05370\r\nDELETIONS:     0.00214\r\nINSERTIONS:    0.00215\r\n```\r\n\r\n```\r\nbash-4.1$ ls\r\nreads.sam  reference.fa  sample_data.fa  test_  \r\nbash-4.1$ ls test_\r\nreads.sam  trash.fasta\r\n```\r\ntest_reads.sam_ext.txt is missing."},"comment":{"url":"https://api.github.com/repos/night-stalker/ERIF/issues/comments/135888734","html_url":"https://github.com/night-stalker/ERIF/issues/2#issuecomment-135888734","issue_url":"https://api.github.com/repos/night-stalker/ERIF/issues/2","id":135888734,"user":{"login":"night-stalker","id":3655162,"avatar_url":"https://avatars.githubusercontent.com/u/3655162?v=3","gravatar_id":"","url":"https://api.github.com/users/night-stalker","html_url":"https://github.com/night-stalker","followers_url":"https://api.github.com/users/night-stalker/followers","following_url":"https://api.github.com/users/night-stalker/following{/other_user}","gists_url":"https://api.github.com/users/night-stalker/gists{/gist_id}","starred_url":"https://api.github.com/users/night-stalker/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/night-stalker/subscriptions","organizations_url":"https://api.github.com/users/night-stalker/orgs","repos_url":"https://api.github.com/users/night-stalker/repos","events_url":"https://api.github.com/users/night-stalker/events{/privacy}","received_events_url":"https://api.github.com/users/night-stalker/received_events","type":"User","site_admin":false},"created_at":"2015-08-28T21:12:05Z","updated_at":"2015-08-28T21:12:05Z","body":"Alignment inside ERIF is not supported anymore. Currently only argument -sam with path to aligned SAM file it will work. "}}