{"action":"opened","issue":{"url":"https://api.github.com/repos/samtools/htsjdk/issues/329","labels_url":"https://api.github.com/repos/samtools/htsjdk/issues/329/labels{/name}","comments_url":"https://api.github.com/repos/samtools/htsjdk/issues/329/comments","events_url":"https://api.github.com/repos/samtools/htsjdk/issues/329/events","html_url":"https://github.com/samtools/htsjdk/issues/329","id":107986133,"number":329,"title":"SequenceUtil.calculateMdAndNmTags does not match other methods","user":{"login":"mattsooknah","id":2549178,"avatar_url":"https://avatars.githubusercontent.com/u/2549178?v=3","gravatar_id":"","url":"https://api.github.com/users/mattsooknah","html_url":"https://github.com/mattsooknah","followers_url":"https://api.github.com/users/mattsooknah/followers","following_url":"https://api.github.com/users/mattsooknah/following{/other_user}","gists_url":"https://api.github.com/users/mattsooknah/gists{/gist_id}","starred_url":"https://api.github.com/users/mattsooknah/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mattsooknah/subscriptions","organizations_url":"https://api.github.com/users/mattsooknah/orgs","repos_url":"https://api.github.com/users/mattsooknah/repos","events_url":"https://api.github.com/users/mattsooknah/events{/privacy}","received_events_url":"https://api.github.com/users/mattsooknah/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-09-23T19:07:58Z","updated_at":"2015-09-23T19:07:58Z","closed_at":null,"body":"As part of the CRAM support, the ```SequenceUtil.calculateMdAndNmTags``` method was added. However it uses a different algorithm for calculating mismatches than, say, ```SequenceUtil.countMismatches```. \r\n\r\nIs there a good reason for having a separate implementation (performance, consistency with samtools, etc)? @vadimzalunin / @jacarey ?\r\n\r\nIf not, I suggest consolidating the code."}}