{"__v":0,"_id":"57d16e4165042a17006683b8","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"},"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":"2016-09-08T13:57:21.240Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":999,"body":"[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"usage: blobtools bamfilter  -b FILE [-i FILE] [-e FILE] [-o PREFIX]\\n                                [--sort] [--keep] [--threads INT] [--gzip]\\n                                [-h|--help]\\n\\n    Options:\\n        -h --help                   show this\\n        -b, --bam FILE              BAM file (sorted by name)\\n        -i, --include FILE          List of contigs whose reads are included\\n                                        (if no FILE is provided ALL mapped reads\\n                                            are included)\\n        -e, --exclude FILE          List of contigs whose reads are excluded\\n                                        (if no FILE is provided ALL mapped reads\\n                                            are included)\\n        --sort                      Sort BAM file by name\\n        --keep                      Keep sorted BAM file (deleted otherwise)\\n        --threads INT               number of sorting/compression threads\\n                                    for sorting [default: 2]\\n        --gzip                      Gzip output\\n        -o, --out PREFIX            Output prefix\\n\",\n      \"language\": \"text\"\n    }\n  ]\n}\n[/block]\nThis tool outputs the following files:\n* PREFIX.BAM.InIn.fq.txt - all bam entries mapping to the contigs listed in the include FILE\n* PREFIX.BAM.InIn.fq - fastq file corresponding to the reads in the file above\n* PREFIX.BAM.ExEx.fq.txt - all bam entries that are in contigs implicitly or explicitly excluded\n* PREFIX.BAM.ExEx.fq - fastq file corresponding to the reads in the file above\n* PREFIX.BAM.info.txt - a summary file with numbers of pairs extracted in the -include and -exclude categories.","excerpt":"","slug":"bamfilter","type":"basic","title":"bamfilter"}
[block:code] { "codes": [ { "code": "usage: blobtools bamfilter -b FILE [-i FILE] [-e FILE] [-o PREFIX]\n [--sort] [--keep] [--threads INT] [--gzip]\n [-h|--help]\n\n Options:\n -h --help show this\n -b, --bam FILE BAM file (sorted by name)\n -i, --include FILE List of contigs whose reads are included\n (if no FILE is provided ALL mapped reads\n are included)\n -e, --exclude FILE List of contigs whose reads are excluded\n (if no FILE is provided ALL mapped reads\n are included)\n --sort Sort BAM file by name\n --keep Keep sorted BAM file (deleted otherwise)\n --threads INT number of sorting/compression threads\n for sorting [default: 2]\n --gzip Gzip output\n -o, --out PREFIX Output prefix\n", "language": "text" } ] } [/block] This tool outputs the following files: * PREFIX.BAM.InIn.fq.txt - all bam entries mapping to the contigs listed in the include FILE * PREFIX.BAM.InIn.fq - fastq file corresponding to the reads in the file above * PREFIX.BAM.ExEx.fq.txt - all bam entries that are in contigs implicitly or explicitly excluded * PREFIX.BAM.ExEx.fq - fastq file corresponding to the reads in the file above * PREFIX.BAM.info.txt - a summary file with numbers of pairs extracted in the -include and -exclude categories.