{"action":"created","issue":{"url":"https://api.github.com/repos/samtools/samtools/issues/369","labels_url":"https://api.github.com/repos/samtools/samtools/issues/369/labels{/name}","comments_url":"https://api.github.com/repos/samtools/samtools/issues/369/comments","events_url":"https://api.github.com/repos/samtools/samtools/issues/369/events","html_url":"https://github.com/samtools/samtools/pull/369","id":64382467,"number":369,"title":"add option -t for turning off translation; add option -p and -i for samtools merge","user":{"login":"ionzhangj8","id":11654322,"avatar_url":"https://avatars.githubusercontent.com/u/11654322?v=3","gravatar_id":"","url":"https://api.github.com/users/ionzhangj8","html_url":"https://github.com/ionzhangj8","followers_url":"https://api.github.com/users/ionzhangj8/followers","following_url":"https://api.github.com/users/ionzhangj8/following{/other_user}","gists_url":"https://api.github.com/users/ionzhangj8/gists{/gist_id}","starred_url":"https://api.github.com/users/ionzhangj8/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ionzhangj8/subscriptions","organizations_url":"https://api.github.com/users/ionzhangj8/orgs","repos_url":"https://api.github.com/users/ionzhangj8/repos","events_url":"https://api.github.com/users/ionzhangj8/events{/privacy}","received_events_url":"https://api.github.com/users/ionzhangj8/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2015-03-25T21:57:38Z","updated_at":"2015-03-26T17:19:18Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/samtools/samtools/pulls/369","html_url":"https://github.com/samtools/samtools/pull/369","diff_url":"https://github.com/samtools/samtools/pull/369.diff","patch_url":"https://github.com/samtools/samtools/pull/369.patch"},"body":"1. Added option -t to turn on/off translation in samtools merge. By default translation is on. If multiple input bam fils contain same RG name or PG name, turning on translation will append some string to RG name or PG name. As a result, if we run the same merge multiple times we'll get different size of output bam files. By turning off translation (using -t0 at command line) will give us identical output bam files, which will behave as samtools-0.1.19.\r\n2. Added option -p for multithreading bam loading in samtools merge. By default there is no extra thread for bam loading. -pN will create N extra threads for bam loading and speed up the process of samtools merge.\r\n3. Add option -i for creating indexing file in samtools merge. When we run samtools merge, if we use option -i [output], the indexing file [output.bai] will be created at the end of merge. Because the data is already in the memory, creating indexing in merge will save us time on running samtools index. Mainly we can save the time of loading the merged bam file for indexing."},"comment":{"url":"https://api.github.com/repos/samtools/samtools/issues/comments/86630504","html_url":"https://github.com/samtools/samtools/pull/369#issuecomment-86630504","issue_url":"https://api.github.com/repos/samtools/samtools/issues/369","id":86630504,"user":{"login":"ionzhangj8","id":11654322,"avatar_url":"https://avatars.githubusercontent.com/u/11654322?v=3","gravatar_id":"","url":"https://api.github.com/users/ionzhangj8","html_url":"https://github.com/ionzhangj8","followers_url":"https://api.github.com/users/ionzhangj8/followers","following_url":"https://api.github.com/users/ionzhangj8/following{/other_user}","gists_url":"https://api.github.com/users/ionzhangj8/gists{/gist_id}","starred_url":"https://api.github.com/users/ionzhangj8/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ionzhangj8/subscriptions","organizations_url":"https://api.github.com/users/ionzhangj8/orgs","repos_url":"https://api.github.com/users/ionzhangj8/repos","events_url":"https://api.github.com/users/ionzhangj8/events{/privacy}","received_events_url":"https://api.github.com/users/ionzhangj8/received_events","type":"User","site_admin":false},"created_at":"2015-03-26T17:19:18Z","updated_at":"2015-03-26T17:19:18Z","body":"We're using samtools 0.1.19. After we switch to samtools 1.2 some of our validation may fail because of using simple diff between old and new merged bam files. I may take option -t out and just use it for our internal purpose.\r\nThanks."}}