{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/1677","repository_url":"https://api.github.com/repos/broadinstitute/gatk","labels_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1677/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1677/comments","events_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1677/events","html_url":"https://github.com/broadinstitute/gatk/pull/1677","id":144980530,"number":1677,"title":"add substring search to smith-waterman and new tests","user":{"login":"gspowley","id":10476709,"avatar_url":"https://avatars.githubusercontent.com/u/10476709?v=3","gravatar_id":"","url":"https://api.github.com/users/gspowley","html_url":"https://github.com/gspowley","followers_url":"https://api.github.com/users/gspowley/followers","following_url":"https://api.github.com/users/gspowley/following{/other_user}","gists_url":"https://api.github.com/users/gspowley/gists{/gist_id}","starred_url":"https://api.github.com/users/gspowley/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gspowley/subscriptions","organizations_url":"https://api.github.com/users/gspowley/orgs","repos_url":"https://api.github.com/users/gspowley/repos","events_url":"https://api.github.com/users/gspowley/events{/privacy}","received_events_url":"https://api.github.com/users/gspowley/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"akiezun","id":1993519,"avatar_url":"https://avatars.githubusercontent.com/u/1993519?v=3","gravatar_id":"","url":"https://api.github.com/users/akiezun","html_url":"https://github.com/akiezun","followers_url":"https://api.github.com/users/akiezun/followers","following_url":"https://api.github.com/users/akiezun/following{/other_user}","gists_url":"https://api.github.com/users/akiezun/gists{/gist_id}","starred_url":"https://api.github.com/users/akiezun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/akiezun/subscriptions","organizations_url":"https://api.github.com/users/akiezun/orgs","repos_url":"https://api.github.com/users/akiezun/repos","events_url":"https://api.github.com/users/akiezun/events{/privacy}","received_events_url":"https://api.github.com/users/akiezun/received_events","type":"User","site_admin":false},"milestone":null,"comments":2,"created_at":"2016-03-31T18:26:55Z","updated_at":"2016-03-31T19:10:20Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/1677","html_url":"https://github.com/broadinstitute/gatk/pull/1677","diff_url":"https://github.com/broadinstitute/gatk/pull/1677.diff","patch_url":"https://github.com/broadinstitute/gatk/pull/1677.patch"},"body":"#1629 @akiezun @droazen @lbergelson\r\nAdded a substring search to `SWPairwiseAlignment.align `to avoid running the full Smith-Waterman when the query is found in the reference without any indels. The performance benefit of this code will be data dependent. In the current HaplotypeCaller test, >80% of the Smith-Waterman calls are filtered by the substring search.\r\n\r\nAdded tests to cover all of the overhang strategies.\r\n\r\n**Note:** The substring search only works for the `SOFTCLIP `and `IGNORE `overhang strategies. The `INDEL `and `LEADING_INDEL `can result in more complicated CIGAR strings. See the `SWPairwiseAlignmentUnitTest.testSubstringMatchIndelLong` and `SWPairwiseAlignmentUnitTest.testSubstringMatchLeadingIndelLong` tests for examples."},"comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/comments/204084351","html_url":"https://github.com/broadinstitute/gatk/pull/1677#issuecomment-204084351","issue_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1677","id":204084351,"user":{"login":"coveralls","id":2354108,"avatar_url":"https://avatars.githubusercontent.com/u/2354108?v=3","gravatar_id":"","url":"https://api.github.com/users/coveralls","html_url":"https://github.com/coveralls","followers_url":"https://api.github.com/users/coveralls/followers","following_url":"https://api.github.com/users/coveralls/following{/other_user}","gists_url":"https://api.github.com/users/coveralls/gists{/gist_id}","starred_url":"https://api.github.com/users/coveralls/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/coveralls/subscriptions","organizations_url":"https://api.github.com/users/coveralls/orgs","repos_url":"https://api.github.com/users/coveralls/repos","events_url":"https://api.github.com/users/coveralls/events{/privacy}","received_events_url":"https://api.github.com/users/coveralls/received_events","type":"User","site_admin":false},"created_at":"2016-03-31T19:10:20Z","updated_at":"2016-03-31T19:10:20Z","body":"\n[![Coverage Status](https://coveralls.io/builds/5618745/badge)](https://coveralls.io/builds/5618745)\n\nCoverage decreased (-72.02%) to 12.14% when pulling **6b9f3c87b4b2ab9887e0fbf33ff6bfac69377a5a on gp_sw_search** into **7df4044607a2cf13223b8f802cbc520cd3dd99a9 on master**.\n"}}