{"action":"created","issue":{"url":"https://api.github.com/repos/aquaskyline/16GT/issues/5","repository_url":"https://api.github.com/repos/aquaskyline/16GT","labels_url":"https://api.github.com/repos/aquaskyline/16GT/issues/5/labels{/name}","comments_url":"https://api.github.com/repos/aquaskyline/16GT/issues/5/comments","events_url":"https://api.github.com/repos/aquaskyline/16GT/issues/5/events","html_url":"https://github.com/aquaskyline/16GT/issues/5","id":304444553,"number":5,"title":"Segmentaiton fault","user":{"login":"KamilSJaron","id":8181573,"avatar_url":"https://avatars1.githubusercontent.com/u/8181573?v=4","gravatar_id":"","url":"https://api.github.com/users/KamilSJaron","html_url":"https://github.com/KamilSJaron","followers_url":"https://api.github.com/users/KamilSJaron/followers","following_url":"https://api.github.com/users/KamilSJaron/following{/other_user}","gists_url":"https://api.github.com/users/KamilSJaron/gists{/gist_id}","starred_url":"https://api.github.com/users/KamilSJaron/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/KamilSJaron/subscriptions","organizations_url":"https://api.github.com/users/KamilSJaron/orgs","repos_url":"https://api.github.com/users/KamilSJaron/repos","events_url":"https://api.github.com/users/KamilSJaron/events{/privacy}","received_events_url":"https://api.github.com/users/KamilSJaron/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2018-03-12T16:27:20Z","updated_at":"2018-03-14T02:27:18Z","closed_at":null,"author_association":"NONE","body":"Hello, I have tried to follow the tutorial in the README file, but program `bam2snapshot` have dropped a a Segmentation fault. Here is `gdb` output :\r\n\r\n```\r\n...\r\nProcessing ref_is350_to_b3v06_masked_div30.bam...\r\n\r\nProgram received signal SIGSEGV, Segmentation fault.\r\n0x0000000000418670 in getAmbPos (chr_id=0, offset=1, ambiguityMap=ambiguityMap@entry=0x6582c0, \r\n    translate=translate@entry=0x7ffff7f4c010, dnaLength=982460096) at indexFunction.cpp:22\r\n22          while (translate[approxValue].startPos > ambPos) {\r\n```\r\n\r\nThe bam file is rather big, but privately I can share it if needed.\r\n\r\n--- edit ---\r\nSome technical details. It's a sorted bamfile, reads were mapped using `bwa-mem` and PCR duplicates were marked using `samblaster`. I am running it on `CentOS 7`, compiled using `gcc version 6.1.1`."},"comment":{"url":"https://api.github.com/repos/aquaskyline/16GT/issues/comments/372883771","html_url":"https://github.com/aquaskyline/16GT/issues/5#issuecomment-372883771","issue_url":"https://api.github.com/repos/aquaskyline/16GT/issues/5","id":372883771,"user":{"login":"aquaskyline","id":895289,"avatar_url":"https://avatars1.githubusercontent.com/u/895289?v=4","gravatar_id":"","url":"https://api.github.com/users/aquaskyline","html_url":"https://github.com/aquaskyline","followers_url":"https://api.github.com/users/aquaskyline/followers","following_url":"https://api.github.com/users/aquaskyline/following{/other_user}","gists_url":"https://api.github.com/users/aquaskyline/gists{/gist_id}","starred_url":"https://api.github.com/users/aquaskyline/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/aquaskyline/subscriptions","organizations_url":"https://api.github.com/users/aquaskyline/orgs","repos_url":"https://api.github.com/users/aquaskyline/repos","events_url":"https://api.github.com/users/aquaskyline/events{/privacy}","received_events_url":"https://api.github.com/users/aquaskyline/received_events","type":"User","site_admin":false},"created_at":"2018-03-14T02:27:18Z","updated_at":"2018-03-14T02:27:18Z","author_association":"OWNER","body":"Working directly with your bam and reference will make my debug faster, but before that, could you please help me to check on one more thing? Could you please check if there exists any alignment with the \"Starting Position + the sum of the numbers in front of tag M, D, =, and X in Cigar String\" exceeding the length of the corresponding scaffold."}}
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