{"action":"closed","issue":{"url":"https://api.github.com/repos/hall-lab/svtyper/issues/37","repository_url":"https://api.github.com/repos/hall-lab/svtyper","labels_url":"https://api.github.com/repos/hall-lab/svtyper/issues/37/labels{/name}","comments_url":"https://api.github.com/repos/hall-lab/svtyper/issues/37/comments","events_url":"https://api.github.com/repos/hall-lab/svtyper/issues/37/events","html_url":"https://github.com/hall-lab/svtyper/issues/37","id":176036631,"number":37,"title":"AttributeError: 'pysam.csamtools.AlignedRead' object has no attribute 'inferred_length'","user":{"login":"bjkelly","id":1202263,"avatar_url":"https://avatars.githubusercontent.com/u/1202263?v=3","gravatar_id":"","url":"https://api.github.com/users/bjkelly","html_url":"https://github.com/bjkelly","followers_url":"https://api.github.com/users/bjkelly/followers","following_url":"https://api.github.com/users/bjkelly/following{/other_user}","gists_url":"https://api.github.com/users/bjkelly/gists{/gist_id}","starred_url":"https://api.github.com/users/bjkelly/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bjkelly/subscriptions","organizations_url":"https://api.github.com/users/bjkelly/orgs","repos_url":"https://api.github.com/users/bjkelly/repos","events_url":"https://api.github.com/users/bjkelly/events{/privacy}","received_events_url":"https://api.github.com/users/bjkelly/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2016-09-09T15:24:25Z","updated_at":"2016-09-09T17:23:48Z","closed_at":"2016-09-09T17:23:48Z","body":"I was originally getting an \"IndexError: list index out of range\" error when using the latest release.  Now that I've updated to the latest master version, I get a \"AttributeError: 'pysam.csamtools.AlignedRead' object has no attribute 'inferred_length'\" error.  \r\n\r\nI have successfully run svtyper on 10 multisample VCFs before this one.  The BAMs were all aligned and processed the same way.  There are two readgroups per BAM, one more represented than the other, but a similar ratio to previous BAMs that have not had an issue.\r\n\r\nBased on some of the info previously requested from similar issues, I have appended some things that may be helpful:\r\n\r\nPython 2.7.5 (default, Jul 24 2013, 15:39:37) \r\n[GCC 4.4.7 20120313 (Red Hat 4.4.7-3)] on linux2\r\nType \"help\", \"copyright\", \"credits\" or \"license\" for more information.\r\n>>> import pkg_resources\r\n>>> pkg_resources.get_distribution(\"pysam\").version\r\n'0.7.5'\r\n\r\n~/apps/svtyper-master/svtyper -B BAMs/sample1.processed.bam ^C BAMs/sample1.splitreads.bam -i sample1.lumpy.vcf -n 2 -M -o sample1.lumpy.gt.vcf --debug\r\n\r\nTraceback (most recent call last):\r\n  File \"/isilon/bgcusers/bjk003/apps/svtyper-master/svtyper\", line 1418, in <module>\r\n    sys.exit(main())\r\n  File \"/isilon/bgcusers/bjk003/apps/svtyper-master/svtyper\", line 1405, in main\r\n    args.debug)\r\n  File \"/isilon/bgcusers/bjk003/apps/svtyper-master/svtyper\", line 1040, in sv_genotype\r\n    sample = Sample.from_bam(bam_list[i], spl_bam_list[i], num_samp, min_lib_prevalence)\r\n  File \"/isilon/bgcusers/bjk003/apps/svtyper-master/svtyper\", line 953, in from_bam\r\n    new_lib = Library.from_bam(lib_name, bam, num_samp)\r\n  File \"/isilon/bgcusers/bjk003/apps/svtyper-master/svtyper\", line 784, in from_bam\r\n    num_samp)\r\n  File \"/isilon/bgcusers/bjk003/apps/svtyper-master/svtyper\", line 727, in __init__\r\n    self.calc_read_length()\r\n  File \"/isilon/bgcusers/bjk003/apps/svtyper-master/svtyper\", line 809, in calc_read_length\r\n    if read.inferred_length > max_rl:\r\nAttributeError: 'pysam.csamtools.AlignedRead' object has no attribute 'inferred_length'"}}
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