{"action":"created","issue":{"url":"https://api.github.com/repos/mahulchak/quickmerge/issues/23","repository_url":"https://api.github.com/repos/mahulchak/quickmerge","labels_url":"https://api.github.com/repos/mahulchak/quickmerge/issues/23/labels{/name}","comments_url":"https://api.github.com/repos/mahulchak/quickmerge/issues/23/comments","events_url":"https://api.github.com/repos/mahulchak/quickmerge/issues/23/events","html_url":"https://github.com/mahulchak/quickmerge/issues/23","id":262997056,"node_id":"MDU6SXNzdWUyNjI5OTcwNTY=","number":23,"title":"Please help. No output, no error, exit 0","user":{"login":"bredeson","id":601458,"node_id":"MDQ6VXNlcjYwMTQ1OA==","avatar_url":"https://avatars3.githubusercontent.com/u/601458?v=4","gravatar_id":"","url":"https://api.github.com/users/bredeson","html_url":"https://github.com/bredeson","followers_url":"https://api.github.com/users/bredeson/followers","following_url":"https://api.github.com/users/bredeson/following{/other_user}","gists_url":"https://api.github.com/users/bredeson/gists{/gist_id}","starred_url":"https://api.github.com/users/bredeson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bredeson/subscriptions","organizations_url":"https://api.github.com/users/bredeson/orgs","repos_url":"https://api.github.com/users/bredeson/repos","events_url":"https://api.github.com/users/bredeson/events{/privacy}","received_events_url":"https://api.github.com/users/bredeson/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2017-10-05T03:52:44Z","updated_at":"2018-09-14T01:06:48Z","closed_at":"2018-09-14T01:06:48Z","author_association":"NONE","body":"Hi Mahul,\r\n\r\nI saw your talk at the PacBio UGM at Standford, read your paper, and wanted to give quickmerge a try. However, I cannot seem to get the program to work and I was hoping you could help me. Probably unrelated: when I compiled quickmerge I get the following warnings:\r\n```#!bash\r\n$ make\r\ng++ -O3 -Wall -o quickmerge quickmerge.cpp qmergelib.cpp -I.\r\nqmergelib.cpp: In function 'void nOvlStoreCalculator(asmMerge&)':\r\nqmergelib.cpp:367:44: warning: 'noRovl' may be used uninitialized in this function [-Wuninitialized]\r\nqmergelib.cpp:367:44: warning: 'noLovl' may be used uninitialized in this function [-Wuninitialized]\r\nqmergelib.cpp: In function 'void discAnchor(std::string&, asmMerge&, std::string&, double)':\r\nqmergelib.cpp:1761:3: warning: 'cutoff' may be used uninitialized in this function [-Wuninitialized]\r\n```\r\n\r\nBeing as these are not critical errors, I tried to run quickmerge anyway on a pre-generated nucmer delta file and it's associated fasta files. quickmerge creates the expected output files with only headers, emits no error messages, and exits with code 0. My command-line was:\r\n```#!bash\r\n$ ~/tools/bin/quickmerge/quickmerge -l 1200000 -hco 5 -c 1.5 -ml 50 -d in.delta -r r.fasta -q q.fasta\r\n```\r\n\r\nMy *de novo* contigs were generated by Canu and my hybrid assembly by DBG2OLC (with some custom contig breaking along the way). I made sure to remove any whitespace in the fasta headers and reformat the fasta sequences to occupy a single line (no line wrapping). Running `merge_wrapper.py --clean_only` creates no ouput (the code block following the conditional statement on line 112 is not evaluated).  \r\n\r\nA snippet of my delta file:\r\n```\r\n$ grep -A 1 '^>' in.delta | head \r\n>tig00002811 Backbone_1000_1_621250 588440 621250\r\n271694 369472 10 97855 296 296 0\r\n--\r\n>tig00007630 Backbone_1000_1_621250 278801 621250\r\n1 20162 316551 336715 80 80 0\r\n--\r\n>tig00008053 Backbone_1000_1_621250 240074 621250\r\n6546 7428 609882 610823 126 126 0\r\n--\r\n>tig00001422 Backbone_1000_1344501_3092750 1131566 1748250\r\n```\r\n\r\nA snippet of my query file:\r\n```#!bash\r\n$ head -2 q.fasta | cut -c1-30\r\n>Backbone_1_1_343250\r\nTCTTTTAAACAAAGTGGAGAACAAAAACTA...\r\n```\r\n\r\nA snippet of my ref file:\r\n```#!bash\r\n$ head -2 r.fasta | cut -c1-30\r\n>tig00000005\r\nATCATCATGGAAGTTCAGCTAGAGGAGTTA...\r\n```\r\n"},"comment":{"url":"https://api.github.com/repos/mahulchak/quickmerge/issues/comments/421198578","html_url":"https://github.com/mahulchak/quickmerge/issues/23#issuecomment-421198578","issue_url":"https://api.github.com/repos/mahulchak/quickmerge/issues/23","id":421198578,"node_id":"MDEyOklzc3VlQ29tbWVudDQyMTE5ODU3OA==","user":{"login":"mahulchak","id":7537640,"node_id":"MDQ6VXNlcjc1Mzc2NDA=","avatar_url":"https://avatars0.githubusercontent.com/u/7537640?v=4","gravatar_id":"","url":"https://api.github.com/users/mahulchak","html_url":"https://github.com/mahulchak","followers_url":"https://api.github.com/users/mahulchak/followers","following_url":"https://api.github.com/users/mahulchak/following{/other_user}","gists_url":"https://api.github.com/users/mahulchak/gists{/gist_id}","starred_url":"https://api.github.com/users/mahulchak/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mahulchak/subscriptions","organizations_url":"https://api.github.com/users/mahulchak/orgs","repos_url":"https://api.github.com/users/mahulchak/repos","events_url":"https://api.github.com/users/mahulchak/events{/privacy}","received_events_url":"https://api.github.com/users/mahulchak/received_events","type":"User","site_admin":false},"created_at":"2018-09-14T01:06:48Z","updated_at":"2018-09-14T01:06:48Z","author_association":"OWNER","body":"@bredeson command line argument order no longer matters in quickmerge. Thanks for your suggestion :)"}}
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