{"action":"created","issue":{"url":"https://api.github.com/repos/samtools/samtools/issues/938","repository_url":"https://api.github.com/repos/samtools/samtools","labels_url":"https://api.github.com/repos/samtools/samtools/issues/938/labels{/name}","comments_url":"https://api.github.com/repos/samtools/samtools/issues/938/comments","events_url":"https://api.github.com/repos/samtools/samtools/issues/938/events","html_url":"https://github.com/samtools/samtools/issues/938","id":356351093,"node_id":"MDU6SXNzdWUzNTYzNTEwOTM=","number":938,"title":"Sorry - Newbie question setting path to directory","user":{"login":"IrsihTypeIII","id":42923653,"node_id":"MDQ6VXNlcjQyOTIzNjUz","avatar_url":"https://avatars0.githubusercontent.com/u/42923653?v=4","gravatar_id":"","url":"https://api.github.com/users/IrsihTypeIII","html_url":"https://github.com/IrsihTypeIII","followers_url":"https://api.github.com/users/IrsihTypeIII/followers","following_url":"https://api.github.com/users/IrsihTypeIII/following{/other_user}","gists_url":"https://api.github.com/users/IrsihTypeIII/gists{/gist_id}","starred_url":"https://api.github.com/users/IrsihTypeIII/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/IrsihTypeIII/subscriptions","organizations_url":"https://api.github.com/users/IrsihTypeIII/orgs","repos_url":"https://api.github.com/users/IrsihTypeIII/repos","events_url":"https://api.github.com/users/IrsihTypeIII/events{/privacy}","received_events_url":"https://api.github.com/users/IrsihTypeIII/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2018-09-03T04:00:45Z","updated_at":"2018-09-03T23:11:09Z","closed_at":null,"author_association":"NONE","body":"Recently changed computers and cannot get Samtools to look in an assigned directory for BAM files.\r\n\r\nI have a need to index BAM files to give me .bam.bai files for analysis.  On a previous computer I  managed somehow to set this up to work but cannot for the life of me get it to work on the new computer.\r\nIt appears I have Cygwin installed correctly together with Samtools and bcftools\r\n\r\nTyping Samtools in the Cygwin Terminal gives me the list of Samtools commands, but entering samtools index file.bam gives me the error:- \r\nopen: No such file or directory\r\n[bam_index_build2] fail to open the BAM file.\r\n\r\nMy files are stored in F:\\My Documents\\Genetics\\Big-Y\\BAM Files\r\n\r\nWhere and what do I set as a Path or Environment Variables in .bash_profile or .bashrc so samtools can find the BAM files.\r\n\r\nSorry for such a newbie question but I am completely lost."},"comment":{"url":"https://api.github.com/repos/samtools/samtools/issues/comments/418203791","html_url":"https://github.com/samtools/samtools/issues/938#issuecomment-418203791","issue_url":"https://api.github.com/repos/samtools/samtools/issues/938","id":418203791,"node_id":"MDEyOklzc3VlQ29tbWVudDQxODIwMzc5MQ==","user":{"login":"IrsihTypeIII","id":42923653,"node_id":"MDQ6VXNlcjQyOTIzNjUz","avatar_url":"https://avatars0.githubusercontent.com/u/42923653?v=4","gravatar_id":"","url":"https://api.github.com/users/IrsihTypeIII","html_url":"https://github.com/IrsihTypeIII","followers_url":"https://api.github.com/users/IrsihTypeIII/followers","following_url":"https://api.github.com/users/IrsihTypeIII/following{/other_user}","gists_url":"https://api.github.com/users/IrsihTypeIII/gists{/gist_id}","starred_url":"https://api.github.com/users/IrsihTypeIII/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/IrsihTypeIII/subscriptions","organizations_url":"https://api.github.com/users/IrsihTypeIII/orgs","repos_url":"https://api.github.com/users/IrsihTypeIII/repos","events_url":"https://api.github.com/users/IrsihTypeIII/events{/privacy}","received_events_url":"https://api.github.com/users/IrsihTypeIII/received_events","type":"User","site_admin":false},"created_at":"2018-09-03T23:11:09Z","updated_at":"2018-09-03T23:11:09Z","author_association":"NONE","body":"I have had a read at the two links provided but they don't seem to directly address my issue.\r\nAdding quotes around the full path did not resolve the issue either.\r\nThe frustrating part is I was able to send a command without defining the path and samtools responded appropriately for three years on the old computer.  I am obviously missing setting a path or environment somewhere, and it this info and assistance I need. "}}
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