{"action":"closed","issue":{"url":"https://api.github.com/repos/jts/sga/issues/118","repository_url":"https://api.github.com/repos/jts/sga","labels_url":"https://api.github.com/repos/jts/sga/issues/118/labels{/name}","comments_url":"https://api.github.com/repos/jts/sga/issues/118/comments","events_url":"https://api.github.com/repos/jts/sga/issues/118/events","html_url":"https://github.com/jts/sga/issues/118","id":156717923,"number":118,"title":"Samtools problem in sga-bam2de.pl","user":{"login":"Katospiegel","id":7240586,"avatar_url":"https://avatars.githubusercontent.com/u/7240586?v=3","gravatar_id":"","url":"https://api.github.com/users/Katospiegel","html_url":"https://github.com/Katospiegel","followers_url":"https://api.github.com/users/Katospiegel/followers","following_url":"https://api.github.com/users/Katospiegel/following{/other_user}","gists_url":"https://api.github.com/users/Katospiegel/gists{/gist_id}","starred_url":"https://api.github.com/users/Katospiegel/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Katospiegel/subscriptions","organizations_url":"https://api.github.com/users/Katospiegel/orgs","repos_url":"https://api.github.com/users/Katospiegel/repos","events_url":"https://api.github.com/users/Katospiegel/events{/privacy}","received_events_url":"https://api.github.com/users/Katospiegel/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2016-05-25T10:39:24Z","updated_at":"2016-07-29T13:02:28Z","closed_at":"2016-07-29T13:02:28Z","body":"Hi, \r\n\r\nTrying to estimate the distances in the sorting sep with sga-bam2de.pl script I found this problem: \r\n\r\n```\r\nsamtools sort libPE.diffcontigs.bam libPE.diffcontigs.sorted.bam\r\n[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files\r\nUsage: samtools sort [options...] [in.bam]\r\nOptions:\r\n  -l INT     Set compression level, from 0 (uncompressed) to 9 (best)\r\n  -m INT     Set maximum memory per thread; suffix K/M/G recognized [768M]\r\n  -n         Sort by read name\r\n  -o FILE    Write final output to FILE rather than standard output\r\n  -T PREFIX  Write temporary files to PREFIX.nnnn.bam\r\n  -@, --threads INT\r\n             Set number of sorting and compression threads [1]\r\n      --input-fmt-option OPT[=VAL]\r\n               Specify a single input file format option in the form\r\n               of OPTION or OPTION=VALUE\r\n  -O, --output-fmt FORMAT[,OPT[=VAL]]...\r\n               Specify output format (SAM, BAM, CRAM)\r\n      --output-fmt-option OPT[=VAL]\r\n               Specify a single output file format option in the form\r\n               of OPTION or OPTION=VALUE\r\n      --reference FILE\r\n               Reference sequence FASTA FILE [null]\r\n```\r\n\r\nI think that is a problem with the samtools version. Trying with the 0.1.19 there is no problem but with the 1.3.1 is neccesary to add **-o** flag to the output in the script:\r\n\r\n```\r\n# sort \r\n$cmd = \"samtools sort $prefix.diffcontigs.bam -o $prefix.diffcontigs.sorted\";\r\n```\r\n\r\nCheers"}}
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