{"action":"closed","issue":{"url":"https://api.github.com/repos/vgteam/vg/issues/301","repository_url":"https://api.github.com/repos/vgteam/vg","labels_url":"https://api.github.com/repos/vgteam/vg/issues/301/labels{/name}","comments_url":"https://api.github.com/repos/vgteam/vg/issues/301/comments","events_url":"https://api.github.com/repos/vgteam/vg/issues/301/events","html_url":"https://github.com/vgteam/vg/issues/301","id":147591855,"number":301,"title":"Behold! The un-index-able graph!","user":{"login":"adamnovak","id":5062495,"avatar_url":"https://avatars2.githubusercontent.com/u/5062495?v=3","gravatar_id":"","url":"https://api.github.com/users/adamnovak","html_url":"https://github.com/adamnovak","followers_url":"https://api.github.com/users/adamnovak/followers","following_url":"https://api.github.com/users/adamnovak/following{/other_user}","gists_url":"https://api.github.com/users/adamnovak/gists{/gist_id}","starred_url":"https://api.github.com/users/adamnovak/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/adamnovak/subscriptions","organizations_url":"https://api.github.com/users/adamnovak/orgs","repos_url":"https://api.github.com/users/adamnovak/repos","events_url":"https://api.github.com/users/adamnovak/events{/privacy}","received_events_url":"https://api.github.com/users/adamnovak/received_events","type":"User","site_admin":false},"labels":[{"id":280142072,"url":"https://api.github.com/repos/vgteam/vg/labels/in%20progress","name":"in progress","color":"ededed","default":false}],"state":"closed","locked":false,"assignee":{"login":"adamnovak","id":5062495,"avatar_url":"https://avatars2.githubusercontent.com/u/5062495?v=3","gravatar_id":"","url":"https://api.github.com/users/adamnovak","html_url":"https://github.com/adamnovak","followers_url":"https://api.github.com/users/adamnovak/followers","following_url":"https://api.github.com/users/adamnovak/following{/other_user}","gists_url":"https://api.github.com/users/adamnovak/gists{/gist_id}","starred_url":"https://api.github.com/users/adamnovak/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/adamnovak/subscriptions","organizations_url":"https://api.github.com/users/adamnovak/orgs","repos_url":"https://api.github.com/users/adamnovak/repos","events_url":"https://api.github.com/users/adamnovak/events{/privacy}","received_events_url":"https://api.github.com/users/adamnovak/received_events","type":"User","site_admin":false},"assignees":[{"login":"adamnovak","id":5062495,"avatar_url":"https://avatars2.githubusercontent.com/u/5062495?v=3","gravatar_id":"","url":"https://api.github.com/users/adamnovak","html_url":"https://github.com/adamnovak","followers_url":"https://api.github.com/users/adamnovak/followers","following_url":"https://api.github.com/users/adamnovak/following{/other_user}","gists_url":"https://api.github.com/users/adamnovak/gists{/gist_id}","starred_url":"https://api.github.com/users/adamnovak/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/adamnovak/subscriptions","organizations_url":"https://api.github.com/users/adamnovak/orgs","repos_url":"https://api.github.com/users/adamnovak/repos","events_url":"https://api.github.com/users/adamnovak/events{/privacy}","received_events_url":"https://api.github.com/users/adamnovak/received_events","type":"User","site_admin":false}],"milestone":null,"comments":14,"created_at":"2016-04-12T00:03:58Z","updated_at":"2017-07-10T17:29:38Z","closed_at":"2017-07-10T17:29:38Z","body":"Here is a graph (kmers.vg in the ZIP file) that can't be indexed with GCSA2. \nNote that this graph validates just fine.\n\n```\n$ vg index -g test.gcsa kmers.vg -k 16\nvg: /cluster/home/anovak/build/vg/include/sdsl/int_vector.hpp:1436: sdsl::int_vector<<anonymous> >::const_reference sdsl::int_vector<<anonymous> >::operator[](const size_type&) const [with unsigned char t_width = 1u; sdsl::int_vector<<anonymous> >::const_reference = const long unsigned int; sdsl::int_vector<<anonymous> >::size_type = long unsigned int]: Assertion `idx < this->size()' failed.\nAborted (core dumped)\n```\n\nThe file was generated like this:\n\n```\nsg2vg http://ga4gh-test1.cloudapp.net/debruijn-mhc-k63/v0.6.g -u | vg view -Jv - | vg mod -X100 - | vg ids -s - > debruijn-mhc-k63.vg\nvg mod -p -l 16 -e 3 debruijn-mhc-k63.vg | vg mod -S -l 32 - > kmers.vg\n```\n\nIt's part of my attempt to run the wiki pipeline on our De Bruijn k63 graph from the bake-off. When indexing the full graph with the De Bruijn .graph file from this graph, I get this same error, and I figured attempting to index the simplified graph was a good sanity check.\n\n[unindexable.zip](https://github.com/vgteam/vg/files/214098/unindexable.zip)\n"}}
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