{"__v":0,"_id":"5798a7d2e8e2090e003b850e","category":{"__v":0,"_id":"57989a8817ced017003c4c69","project":"57618347b65324200072d6a5","version":"57618347b65324200072d6a8","sync":{"url":"","isSync":false},"reference":false,"createdAt":"2016-07-27T11:27:04.750Z","from_sync":false,"order":3,"slug":"docstrings","title":"Documentation"},"parentDoc":null,"project":"57618347b65324200072d6a5","user":"57617c8caa540f3600bfed20","version":{"__v":8,"_id":"57618347b65324200072d6a8","project":"57618347b65324200072d6a5","createdAt":"2016-06-15T16:33:11.587Z","releaseDate":"2016-06-15T16:33:11.587Z","categories":["57618347b65324200072d6a9","5761912d207db7170022fbe9","57619455a7c9f729009a74e0","576e8ae1f37ab41700147471","5797b8e5209a6e0e00b8321b","57989a8817ced017003c4c69","579ca6f3d46f960e0029a8ec","579ca703fefb1d0e00c94f06"],"is_deprecated":false,"is_hidden":false,"is_beta":false,"is_stable":true,"codename":"blobtools v0.9.19","version_clean":"0.9.19","version":"0.9.19"},"updates":[],"next":{"pages":[],"description":""},"createdAt":"2016-07-27T12:23:46.740Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":4,"body":"[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"usage: blobtools map2cov         -i FASTA [-b BAM...] [-a CAS...] [-s SAM...]\\n                                    [-o PREFIX] [--no_base_cov]\\n                                    [-h|--help]\\n\\n    Options:\\n        -h --help                   show this\\n        -i, --infile FASTA          FASTA file of assembly. Headers are split at whitespaces.\\n        -b, --bam <BAM>...          BAM file (requires samtools in $PATH)\\n        -a, --cas <CAS>...          CAS file (requires clc_mapping_info in $PATH)\\n        -s, --sam <SAM>...          SAM file\\n        -o, --output <PREFIX>       Output prefix\\n        --no_base_cov               only parse read coverage (faster, but ...\\n                                        can only be used for \\\"blobtools blobplot --noblobs\\\")\",\n      \"language\": \"text\"\n    }\n  ]\n}\n[/block]","excerpt":"","slug":"map2cov","type":"basic","title":"map2cov"}
[block:code] { "codes": [ { "code": "usage: blobtools map2cov -i FASTA [-b BAM...] [-a CAS...] [-s SAM...]\n [-o PREFIX] [--no_base_cov]\n [-h|--help]\n\n Options:\n -h --help show this\n -i, --infile FASTA FASTA file of assembly. Headers are split at whitespaces.\n -b, --bam <BAM>... BAM file (requires samtools in $PATH)\n -a, --cas <CAS>... CAS file (requires clc_mapping_info in $PATH)\n -s, --sam <SAM>... SAM file\n -o, --output <PREFIX> Output prefix\n --no_base_cov only parse read coverage (faster, but ...\n can only be used for \"blobtools blobplot --noblobs\")", "language": "text" } ] } [/block]