{"action":"closed","issue":{"url":"https://api.github.com/repos/isovic/graphmap/issues/19","repository_url":"https://api.github.com/repos/isovic/graphmap","labels_url":"https://api.github.com/repos/isovic/graphmap/issues/19/labels{/name}","comments_url":"https://api.github.com/repos/isovic/graphmap/issues/19/comments","events_url":"https://api.github.com/repos/isovic/graphmap/issues/19/events","html_url":"https://github.com/isovic/graphmap/issues/19","id":147278935,"number":19,"title":"Effect of -F option","user":{"login":"rrwick","id":7053555,"avatar_url":"https://avatars.githubusercontent.com/u/7053555?v=3","gravatar_id":"","url":"https://api.github.com/users/rrwick","html_url":"https://github.com/rrwick","followers_url":"https://api.github.com/users/rrwick/followers","following_url":"https://api.github.com/users/rrwick/following{/other_user}","gists_url":"https://api.github.com/users/rrwick/gists{/gist_id}","starred_url":"https://api.github.com/users/rrwick/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rrwick/subscriptions","organizations_url":"https://api.github.com/users/rrwick/orgs","repos_url":"https://api.github.com/users/rrwick/repos","events_url":"https://api.github.com/users/rrwick/events{/privacy}","received_events_url":"https://api.github.com/users/rrwick/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":8,"created_at":"2016-04-10T23:35:30Z","updated_at":"2016-04-22T09:44:38Z","closed_at":"2016-04-22T09:44:38Z","body":"I noticed odd behaviour with the `-F` option, and I'm not sure if this is a bug or if I'm misinterpreting the algorithm. My understanding was that a higher `-F` value would potentially lead to more alignments as it lowered the score threshold, and a value of 1.0 would potentially give the most alignments, effectively not using a score threshold. But I've encountered a case where increasing the `-F` value reduces my alignments.\r\n\r\nHere are some example files to replicate what I'm seeing.\r\n[contig.fasta.txt](https://github.com/isovic/graphmap/files/212067/contig.fasta.txt) - 3 kb reference\r\n[reads.fastq.txt](https://github.com/isovic/graphmap/files/212069/reads.fastq.txt) - two reads\r\n\r\nThis command produces two alignments (one for each read):\r\n`graphmap -r contig.fasta.txt -d reads.fastq.txt -o out.sam -Z -F 0.9`\r\n\r\nIncreasing the `-F` value to 0.99 produces only one alignment:\r\n`graphmap -r contig.fasta.txt -d reads.fastq.txt -o out.sam -Z -F 0.99`\r\n\r\nAnd an even higher `-F` value results in no alignments:\r\n`graphmap -r contig.fasta.txt -d reads.fastq.txt -o out.sam -Z -F 0.999`\r\n\r\nI only see this behaviour with the default `anchor` algorithm. The `anchorgotoh` algorithm behaves more as expected, where increasing `-F` value towards 1.0 results in a third alignment (two for one read). I'm using the [2e314e6](https://github.com/isovic/graphmap/commit/2e314e61be3fe8f80aa5038bd5bfb2a76a191b49) commit (most current of the extanchorend branch).\r\n\r\n\r\n"}}