| 9 | #include "CommonHelp.h" |
| 10 | |
| 11 | void complement_help(void) { |
| 12 | |
| 13 | cerr << "\nTool: bedtools complement (aka complementBed)" << endl; |
| 14 | cerr << "Version: " << VERSION << "\n"; |
| 15 | cerr << "Summary: Returns the base pair complement of a feature file." << endl << endl; |
| 16 | |
| 17 | cerr << "Usage: " << "bedtools complement" << " [OPTIONS] -i <bed/gff/vcf> -g <genome>" << endl << endl; |
| 18 | |
| 19 | cerr << "Options: " << endl; |
| 20 | |
| 21 | cerr << "\t-L\t" << "Limit output to solely the chromosomes with records in the input file." << endl << endl; |
| 22 | |
| 23 | cerr << "Notes: " << endl; |
| 24 | cerr << "\t(1) The genome file should tab delimited and structured as follows:" << endl; |
| 25 | cerr << "\t <chromName><TAB><chromSize>" << endl << endl; |
| 26 | cerr << "\tFor example, Human (hg19):" << endl; |
| 27 | cerr << "\tchr1\t249250621" << endl; |
| 28 | cerr << "\tchr2\t243199373" << endl; |
| 29 | cerr << "\t..." << endl; |
| 30 | cerr << "\tchr18_gl000207_random\t4262" << endl << endl; |
| 31 | |
| 32 | cerr << "Tip 1. Use samtools faidx to create a genome file from a FASTA: " << endl; |
| 33 | cerr << "\tOne can the samtools faidx command to index a FASTA file." << endl; |
| 34 | cerr << "\tThe resulting .fai index is suitable as a genome file, " << endl; |
| 35 | cerr << "\tas bedtools will only look at the first two, relevant columns" << endl; |
| 36 | cerr << "\tof the .fai file." << endl << endl; |
| 37 | cerr << "\tFor example:" << endl; |
| 38 | cerr << "\tsamtools faidx GRCh38.fa" << endl; |
| 39 | cerr << "\tbedtools complement -i my.bed -g GRCh38.fa.fai" << endl << endl; |
| 40 | |
| 41 | cerr << "Tip 2. Use UCSC Table Browser to create a genome file: " << endl; |
| 42 | cerr << "\tOne can use the UCSC Genome Browser's MySQL database to extract" << endl; |
| 43 | cerr << "\tchromosome sizes. For example, H. sapiens:" << endl << endl; |
| 44 | cerr << "\tmysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \\" << endl; |
| 45 | cerr << "\t\"select chrom, size from hg19.chromInfo\" > hg19.genome" << endl << endl; |
| 46 | |
| 47 | |
| 48 | |
| 49 | } |