{"action":"opened","issue":{"url":"https://api.github.com/repos/jaxcs/Seqnature/issues/4","repository_url":"https://api.github.com/repos/jaxcs/Seqnature","labels_url":"https://api.github.com/repos/jaxcs/Seqnature/issues/4/labels{/name}","comments_url":"https://api.github.com/repos/jaxcs/Seqnature/issues/4/comments","events_url":"https://api.github.com/repos/jaxcs/Seqnature/issues/4/events","html_url":"https://github.com/jaxcs/Seqnature/issues/4","id":170695533,"number":4,"title":"Issue with getting all indels being incorporated","user":{"login":"juanfmacias3","id":2448982,"avatar_url":"https://avatars.githubusercontent.com/u/2448982?v=3","gravatar_id":"","url":"https://api.github.com/users/juanfmacias3","html_url":"https://github.com/juanfmacias3","followers_url":"https://api.github.com/users/juanfmacias3/followers","following_url":"https://api.github.com/users/juanfmacias3/following{/other_user}","gists_url":"https://api.github.com/users/juanfmacias3/gists{/gist_id}","starred_url":"https://api.github.com/users/juanfmacias3/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/juanfmacias3/subscriptions","organizations_url":"https://api.github.com/users/juanfmacias3/orgs","repos_url":"https://api.github.com/users/juanfmacias3/repos","events_url":"https://api.github.com/users/juanfmacias3/events{/privacy}","received_events_url":"https://api.github.com/users/juanfmacias3/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-08-11T17:02:57Z","updated_at":"2016-08-11T17:02:57Z","closed_at":null,"body":"So I am trying to figure out how to use this program and I decided to make some fake data to test it all out. I created a fake genome and some VCF files to along with it. \r\n\r\nIndels:\r\n<img width=\"745\" alt=\"Indels\" src=\"https://cloud.githubusercontent.com/assets/2448982/17597276/a4036690-5fba-11e6-9bc3-bb7fece90f83.png\">\r\n\r\nSNPS:\r\n<img width=\"750\" alt=\"SNPs\" src=\"https://cloud.githubusercontent.com/assets/2448982/17597307/c62823f0-5fba-11e6-9670-aec6c7782e6b.png\">\r\n\r\nfakeGenome:\r\n<img width=\"433\" alt=\"Genome\" src=\"https://cloud.githubusercontent.com/assets/2448982/17597326/dfa5c3e6-5fba-11e6-88db-95710d50c86d.png\">\r\n\r\nI run the program like so:\r\n\r\nbuild_new_sequence_from_vcfs.py -r fakeGenome.fa -s SNPS.vcf -i Indels.vcf -o replaced.fa LG\r\n\r\nIt appears to make most of the changes, but does not make the last indel change.\r\n\r\n<img width=\"736\" alt=\"alignment\" src=\"https://cloud.githubusercontent.com/assets/2448982/17597426/532e3abe-5fbb-11e6-8926-8a181cd1d515.png\">\r\n\r\nAm I missing anything simple? Is it because it is near the end of the sequence?"}}
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