{"action":"opened","issue":{"url":"https://api.github.com/repos/bjpop/rover/issues/8","labels_url":"https://api.github.com/repos/bjpop/rover/issues/8/labels{/name}","comments_url":"https://api.github.com/repos/bjpop/rover/issues/8/comments","events_url":"https://api.github.com/repos/bjpop/rover/issues/8/events","html_url":"https://github.com/bjpop/rover/issues/8","id":67139491,"number":8,"title":"Problems with bam file","user":{"login":"marcelcaraciolo","id":275084,"avatar_url":"https://avatars.githubusercontent.com/u/275084?v=3","gravatar_id":"","url":"https://api.github.com/users/marcelcaraciolo","html_url":"https://github.com/marcelcaraciolo","followers_url":"https://api.github.com/users/marcelcaraciolo/followers","following_url":"https://api.github.com/users/marcelcaraciolo/following{/other_user}","gists_url":"https://api.github.com/users/marcelcaraciolo/gists{/gist_id}","starred_url":"https://api.github.com/users/marcelcaraciolo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/marcelcaraciolo/subscriptions","organizations_url":"https://api.github.com/users/marcelcaraciolo/orgs","repos_url":"https://api.github.com/users/marcelcaraciolo/repos","events_url":"https://api.github.com/users/marcelcaraciolo/events{/privacy}","received_events_url":"https://api.github.com/users/marcelcaraciolo/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-04-08T14:11:57Z","updated_at":"2015-04-08T14:11:57Z","closed_at":null,"body":"Hello guys,\r\n\r\nFirst of all, good work! I am trying to use the tool for one of our bam files and it is giving us an IndexError  during the cigar reading step at your code.  The following traceback:\r\n\r\n```\r\n./rover/rover/rover.py --primers KRASNRAS.bed  --out variants_rover.vcf --proportionthresh 0.05 --overlap 0.9 --absthresh 2 --id_info dbsnp_138.hg19.vcf ./Miseq-03-04-15/KRASNRAS/164180_4/alignments/164180_4_001_L001_1.realigned.recal.bam\r\nWARNING:root:Read M00538:83:000000000-D0CJD:1:1101:8832:16146 with no pair\r\nWARNING:root:Read M00538:83:000000000-D0CJD:1:1101:15624:2194 with no pair\r\nWARNING:root:Read M00538:83:000000000-D0CJD:1:1101:14841:2252 with no pair\r\nWARNING:root:Read M00538:83:000000000-D0CJD:1:1102:27778:18791 with no pair\r\nTraceback (most recent call last):\r\n  File \"./rover/rover/rover.py\", line 913, in <module>\r\n    main()\r\n  File \"./rover/rover/rover.py\", line 910, in main\r\n    process_bams(args)\r\n  File \"./rover/rover/rover.py\", line 892, in process_bams\r\n    total_data, vcf_reader)\r\n  File \"./rover/rover/rover.py\", line 630, in process_blocks\r\n    parse_md(get_md(read2), []))\r\n  File \"./rover/rover/rover.py\", line 163, in read_variants\r\n    context = aligned_bases[seq_index + next_md.size - 1].base\r\nIndexError: list index out of range\r\n```\r\n"}}