{"action":"created","issue":{"url":"https://api.github.com/repos/BauerLab/ngsane/issues/48","labels_url":"https://api.github.com/repos/BauerLab/ngsane/issues/48/labels{/name}","comments_url":"https://api.github.com/repos/BauerLab/ngsane/issues/48/comments","events_url":"https://api.github.com/repos/BauerLab/ngsane/issues/48/events","html_url":"https://github.com/BauerLab/ngsane/issues/48","id":81869301,"number":48,"title":"bug in hicupCountInteractions.py","user":{"login":"xflicsu","id":5843308,"avatar_url":"https://avatars.githubusercontent.com/u/5843308?v=3","gravatar_id":"","url":"https://api.github.com/users/xflicsu","html_url":"https://github.com/xflicsu","followers_url":"https://api.github.com/users/xflicsu/followers","following_url":"https://api.github.com/users/xflicsu/following{/other_user}","gists_url":"https://api.github.com/users/xflicsu/gists{/gist_id}","starred_url":"https://api.github.com/users/xflicsu/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/xflicsu/subscriptions","organizations_url":"https://api.github.com/users/xflicsu/orgs","repos_url":"https://api.github.com/users/xflicsu/repos","events_url":"https://api.github.com/users/xflicsu/events{/privacy}","received_events_url":"https://api.github.com/users/xflicsu/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-05-28T10:36:32Z","updated_at":"2015-05-29T01:41:49Z","closed_at":null,"body":"Hello ngsane designers,\r\nI have install ngsane to deal with HiC-seq datasets.\r\nThere may be an bug in hicupCountInteractions.py\r\n##########################\r\npython /usr/packages/ngsane/0.5.0.3//tools/hicupCountInteractions.py --verbose --genomeFragmentFile=/usr/packages/ngsane/0.5.0.3/smokebox/common/hicup/Digest_hg19_Ncol_none.txt --outputDir=/usr/packages/ngsane/0.5.0.3/smokebox/HiC/hicup/ /usr/packages/ngsane/0.5.0.3/smokebox/HiC/hicup/GMall_Ncol_uniques.bam\r\n\r\n###########################################################################\r\nTraceback (most recent call last):\r\n  File \"/usr/packages/ngsane/0.5.0.3//tools/hicupCountInteractions.py\", line 415, in <module>\r\n    main()\r\n  File \"/usr/packages/ngsane/0.5.0.3//tools/hicupCountInteractions.py\", line 141, in main\r\n    process()\r\n  File \"/usr/packages/ngsane/0.5.0.3//tools/hicupCountInteractions.py\", line 407, in process\r\n    [ fragmentList, fragmentPairs ] = countReadsPerFragment(intersect_tree)\r\n  File \"/usr/packages/ngsane/0.5.0.3//tools/hicupCountInteractions.py\", line 316, in countReadsPerFragment\r\n    readpair = findNextReadPair(samiter)\r\n  File \"/usr/packages/ngsane/0.5.0.3//tools/hicupCountInteractions.py\", line 242, in findNextReadPair\r\n    readpair=[getNext(samiter), getNext(samiter)]\r\n  File \"/usr/packages/ngsane/0.5.0.3//tools/hicupCountInteractions.py\", line 231, in getNext\r\n    return Read(iterator.next())\r\n  File \"/usr/packages/ngsane/0.5.0.3//tools/hicupCountInteractions.py\", line 24, in __init__\r\n    if (read==\"\"):\r\nTypeError: Argument 'other' has incorrect type (expected pysam.calignmentfile.AlignedSegment, got str)\r\n\r\n##################################\r\nSo, how to fix this bug?\r\nThanks for your attention!"},"comment":{"url":"https://api.github.com/repos/BauerLab/ngsane/issues/comments/106652176","html_url":"https://github.com/BauerLab/ngsane/issues/48#issuecomment-106652176","issue_url":"https://api.github.com/repos/BauerLab/ngsane/issues/48","id":106652176,"user":{"login":"xflicsu","id":5843308,"avatar_url":"https://avatars.githubusercontent.com/u/5843308?v=3","gravatar_id":"","url":"https://api.github.com/users/xflicsu","html_url":"https://github.com/xflicsu","followers_url":"https://api.github.com/users/xflicsu/followers","following_url":"https://api.github.com/users/xflicsu/following{/other_user}","gists_url":"https://api.github.com/users/xflicsu/gists{/gist_id}","starred_url":"https://api.github.com/users/xflicsu/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/xflicsu/subscriptions","organizations_url":"https://api.github.com/users/xflicsu/orgs","repos_url":"https://api.github.com/users/xflicsu/repos","events_url":"https://api.github.com/users/xflicsu/events{/privacy}","received_events_url":"https://api.github.com/users/xflicsu/received_events","type":"User","site_admin":false},"created_at":"2015-05-29T01:41:48Z","updated_at":"2015-05-29T01:41:48Z","body":"Hello, I find the error result from \"samtools sort\" command. My system have installed a previous version.   When I change to 1.1, it works well. Thanks!"}}