{"action":"created","issue":{"url":"https://api.github.com/repos/vsbuffalo/readphaser/issues/4","labels_url":"https://api.github.com/repos/vsbuffalo/readphaser/issues/4/labels{/name}","comments_url":"https://api.github.com/repos/vsbuffalo/readphaser/issues/4/comments","events_url":"https://api.github.com/repos/vsbuffalo/readphaser/issues/4/events","html_url":"https://github.com/vsbuffalo/readphaser/issues/4","id":64738768,"number":4,"title":"error while running readphaser","user":{"login":"joqb","id":11645116,"avatar_url":"https://avatars.githubusercontent.com/u/11645116?v=3","gravatar_id":"","url":"https://api.github.com/users/joqb","html_url":"https://github.com/joqb","followers_url":"https://api.github.com/users/joqb/followers","following_url":"https://api.github.com/users/joqb/following{/other_user}","gists_url":"https://api.github.com/users/joqb/gists{/gist_id}","starred_url":"https://api.github.com/users/joqb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/joqb/subscriptions","organizations_url":"https://api.github.com/users/joqb/orgs","repos_url":"https://api.github.com/users/joqb/repos","events_url":"https://api.github.com/users/joqb/events{/privacy}","received_events_url":"https://api.github.com/users/joqb/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":12,"created_at":"2015-03-27T10:55:34Z","updated_at":"2015-04-16T18:07:31Z","closed_at":null,"body":"Hi,\r\n\r\nI'm trying to get to get readphaser running. For the moment I'm experiencing on the HAPCUT test data.\r\nhere is the error I got:\r\n\r\n-bash-4.2$ pr.py NA18508.chr20.test.bam.hapcut NA18508.chr20.test.bam\r\n[phase_reads] opening alignment BAM file...\tdone.\r\n[phase_reads] phasing '20', block_id 0\r\nTraceback (most recent call last):\r\n  File \"/opt/Bio/readphaser/20150325/bin/pr.py\", line 365, in <module>\r\n    output_main(args)\r\n  File \"/opt/Bio/readphaser/20150325/bin/pr.py\", line 335, in output_main\r\n    region=args.region)\r\n  File \"/opt/Bio/readphaser/20150325/bin/pr.py\", line 298, in phase_reads\r\n    group_reads_by_block(reads, block, block_id, callback, stats, inconsistent_counts_file)\r\n  File \"/opt/Bio/readphaser/20150325/bin/pr.py\", line 212, in group_reads_by_block\r\n    htype_pos = group_varpos_by_haplotype(readpair, haplotypes, allele_counts)\r\n  File \"/opt/Bio/readphaser/20150325/bin/pr.py\", line 147, in group_varpos_by_haplotype\r\n    if read.overlap(interval[0], interval[1]) == allele_len:\r\nTypeError: overlap() takes no arguments (2 given)\r\n\r\nCheers,\r\nNath\r\n"},"comment":{"url":"https://api.github.com/repos/vsbuffalo/readphaser/issues/comments/93804562","html_url":"https://github.com/vsbuffalo/readphaser/issues/4#issuecomment-93804562","issue_url":"https://api.github.com/repos/vsbuffalo/readphaser/issues/4","id":93804562,"user":{"login":"iamcorrinne","id":6353236,"avatar_url":"https://avatars.githubusercontent.com/u/6353236?v=3","gravatar_id":"","url":"https://api.github.com/users/iamcorrinne","html_url":"https://github.com/iamcorrinne","followers_url":"https://api.github.com/users/iamcorrinne/followers","following_url":"https://api.github.com/users/iamcorrinne/following{/other_user}","gists_url":"https://api.github.com/users/iamcorrinne/gists{/gist_id}","starred_url":"https://api.github.com/users/iamcorrinne/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/iamcorrinne/subscriptions","organizations_url":"https://api.github.com/users/iamcorrinne/orgs","repos_url":"https://api.github.com/users/iamcorrinne/repos","events_url":"https://api.github.com/users/iamcorrinne/events{/privacy}","received_events_url":"https://api.github.com/users/iamcorrinne/received_events","type":"User","site_admin":false},"created_at":"2015-04-16T18:07:31Z","updated_at":"2015-04-16T18:07:31Z","body":"Nope.  \r\n\r\n>>> import pysam\r\n>>> pysam.__version__\r\n'0.8.2.1'\r\n\r\n"}}