/*****************************************************************************
bedtools.cpp
bedtools command line interface.
Thanks to Heng Li, as this interface is inspired and
based upon his samtools interface.
(c) 2009-2011 - Aaron Quinlan
Quinlan Laboratory
Department of Public Health Sciences
Center for Public Health genomics
University of Virginia
aaronquinlan@gmail.com
Licenced under the GNU General Public License 2.0 license.
******************************************************************************/
#include <iostream>
#include <fstream>
#include <stdlib.h>
#include <string>
#include "version.h"
using namespace std;
// define our program name
#define PROGRAM_NAME "bedtools"
// colors for the term's menu
#define RESET "\033[m"
#define GREEN "\033[1;32m"
#define BLUE "\033[1;34m"
#define RED "\033[1;31m"
// define our parameter checking macro
#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
int annotate_main(int argc, char* argv[]);//
int bamtobed_main(int argc, char* argv[]);//
int bamtofastq_main(int argc, char* argv[]);//
int bed12tobed6_main(int argc, char* argv[]); //
int bedtobam_main(int argc, char* argv[]);//
int bedtoigv_main(int argc, char* argv[]);//
int bedpetobam_main(int argc, char* argv[]);//
int closest_main(int argc, char* argv[]); //
int cluster_main(int argc, char* argv[]); //
int complement_main(int argc, char* argv[]);//
int coverage_main(int argc, char* argv[]); //
int regress_test_main(int argc, char **argv); //
int expand_main(int argc, char* argv[]);//
int fastafrombed_main(int argc, char* argv[]);//
int flank_main(int argc, char* argv[]); //
int genomecoverage_main(int argc, char* argv[]);//
int getoverlap_main(int argc, char* argv[]);//
int groupby_main(int argc, char* argv[]);//
int intersect_main(int argc, char* argv[]); //
int jaccard_main(int argc, char* argv[]); //
int links_main(int argc, char* argv[]);//
int maskfastafrombed_main(int argc, char* argv[]);//
int map_main(int argc, char* argv[]); //
int merge_main(int argc, char* argv[]); //
int multibamcov_main(int argc, char* argv[]);//
int multiintersect_main(int argc, char* argv[]);//
int nek_sandbox1_main(int argc, char* argv[]);//
int nuc_main(int argc, char* argv[]);//
int pairtobed_main(int argc, char* argv[]);//
int pairtopair_main(int argc, char* argv[]);//
int random_main(int argc, char* argv[]); //
int reldist_main(int argc, char* argv[]); //
int shuffle_main(int argc, char* argv[]); //
int slop_main(int argc, char* argv[]); //
int sort_main(int argc, char* argv[]); //
int subtract_main(int argc, char* argv[]); //
int tagbam_main(int argc, char* argv[]);//
int unionbedgraphs_main(int argc, char* argv[]);//
int window_main(int argc, char* argv[]); //
int windowmaker_main(int argc, char* argv[]); //
int bedtools_help(void);
int bedtools_faq(void);
int main(int argc, char *argv[])
{
// make sure the user at least entered a sub_command
if (argc < 2) return bedtools_help();
std::string sub_cmd = argv[1];
// genome arithmetic tools
if (sub_cmd == "intersect") return intersect_main(argc-1, argv+1);
else if (sub_cmd == "window") return window_main(argc-1, argv+1);
else if (sub_cmd == "closest") return closest_main(argc-1, argv+1);
else if (sub_cmd == "coverage") return coverage_main(argc-1, argv+1);
else if (sub_cmd == "map") return map_main(argc-1, argv+1);
else if (sub_cmd == "genomecov") return genomecoverage_main(argc-1, argv+1);
else if (sub_cmd == "merge") return merge_main(argc-1, argv+1);
else if (sub_cmd == "cluster") return cluster_main(argc-1, argv+1);
else if (sub_cmd == "complement") return complement_main(argc-1, argv+1);
else if (sub_cmd == "subtract") return subtract_main(argc-1, argv+1);
else if (sub_cmd == "slop") return slop_main(argc-1, argv+1);
else if (sub_cmd == "flank") return flank_main(argc-1, argv+1);
else if (sub_cmd == "sort") return sort_main(argc-1, argv+1);
else if (sub_cmd == "random") return random_main(argc-1, argv+1);
else if (sub_cmd == "shuffle") return shuffle_main(argc-1, argv+1);
else if (sub_cmd == "annotate") return annotate_main(argc-1, argv+1);
// Multi-way file comparisonstools
else if (sub_cmd == "multiinter") return multiintersect_main(argc-1, argv+1);
else if (sub_cmd == "unionbedg") return unionbedgraphs_main(argc-1, argv+1);
// paired-end conversion tools
else if (sub_cmd == "pairtobed") return pairtobed_main(argc-1, argv+1);
else if (sub_cmd == "pairtopair") return pairtopair_main(argc-1, argv+1);
// format conversion tools
else if (sub_cmd == "bamtobed") return bamtobed_main(argc-1, argv+1);
else if (sub_cmd == "bedtobam") return bedtobam_main(argc-1, argv+1);
else if (sub_cmd == "bamtofastq") return bamtofastq_main(argc-1, argv+1);
else if (sub_cmd == "bedpetobam") return bedpetobam_main(argc-1, argv+1);
else if (sub_cmd == "bed12tobed6") return bed12tobed6_main(argc-1, argv+1);
// BAM-specific tools
else if (sub_cmd == "multicov") return multibamcov_main(argc-1, argv+1);
else if (sub_cmd == "tag") return tagbam_main(argc-1, argv+1);
// fasta tools
else if (sub_cmd == "getfasta") return fastafrombed_main(argc-1, argv+1);
else if (sub_cmd == "maskfasta") return maskfastafrombed_main(argc-1, argv+1);
else if (sub_cmd == "nuc") return nuc_main(argc-1, argv+1);
// statistics tools
else if (sub_cmd == "jaccard") return jaccard_main(argc-1, argv+1);
else if (sub_cmd == "reldist") return reldist_main(argc-1, argv+1);
// misc. tools
else if (sub_cmd == "overlap") return getoverlap_main(argc-1, argv+1);
else if (sub_cmd == "igv") return bedtoigv_main(argc-1, argv+1);
else if (sub_cmd == "links") return links_main(argc-1, argv+1);
else if (sub_cmd == "makewindows") return windowmaker_main(argc-1, argv+1);
else if (sub_cmd == "groupby") return groupby_main(argc-1, argv+1);
else if (sub_cmd == "expand") return expand_main(argc-1, argv+1);
else if (sub_cmd == "neksb1") return nek_sandbox1_main(argc-1, argv+1);
else if (sub_cmd == "regresstest") return regress_test_main(argc, argv); //this command does need all the orig args.
// help
else if (sub_cmd == "-h" || sub_cmd == "--help" ||
sub_cmd == "-help")
return bedtools_help();
// frequently asked questions
else if (sub_cmd == "--FAQ" || sub_cmd == "--faq" ||
sub_cmd == "-FAQ" || sub_cmd == "-faq")
return bedtools_faq();
// verison information
else if (sub_cmd == "-version" || sub_cmd == "--version")
cout << "bedtools " << VERSION << endl;
// verison information
else if (sub_cmd == "-contact" || sub_cmd == "--contact")
{
cout << endl;
cout << "- For further help, or to report a bug, please " << endl;
cout << " email the bedtools mailing list: " << endl;
cout << " bedtools-discuss@googlegroups.com" << endl << endl;
cout << "- Stable releases of bedtools can be found at: " << endl;
cout << " http://bedtools.googlecode.com" << endl << endl;
cout << "- The development repository can be found at: " << endl;
cout << " https://github.com/arq5x/bedtools" << endl << endl;
}
// unknown
else {
// TODO: Implement a Levenstein-based "did you mean???"
cerr << "error: unrecognized command: " << argv[1] << endl << endl;
return 1;
}
return 0;
}
int bedtools_help(void)
{
cout << PROGRAM_NAME << ": flexible tools for genome arithmetic and DNA sequence analysis.\n";
cout << "usage: bedtools <subcommand> [options]" << endl << endl;
cout << "The bedtools sub-commands include:" << endl;
cout << endl;
cout << "[ Genome arithmetic ]" << endl;
cout << " intersect " << "Find overlapping intervals in various ways.\n";
cout << " window " << "Find overlapping intervals within a window around an interval.\n";
cout << " closest " << "Find the closest, potentially non-overlapping interval.\n";
cout << " coverage " << "Compute the coverage over defined intervals.\n";
cout << " map " << "Apply a function to a column for each overlapping interval.\n";
cout << " genomecov " << "Compute the coverage over an entire genome.\n";
cout << " merge " << "Combine overlapping/nearby intervals into a single interval.\n";
cout << " cluster " << "Cluster (but don't merge) overlapping/nearby intervals.\n";
cout << " complement " << "Extract intervals _not_ represented by an interval file.\n";
cout << " subtract " << "Remove intervals based on overlaps b/w two files.\n";
cout << " slop " << "Adjust the size of intervals.\n";
cout << " flank " << "Create new intervals from the flanks of existing intervals.\n";
cout << " sort " << "Order the intervals in a file.\n";
cout << " random " << "Generate random intervals in a genome.\n";
cout << " shuffle " << "Randomly redistrubute intervals in a genome.\n";
cout << " annotate " << "Annotate coverage of features from multiple files.\n";
cout << endl;
cout << "[ Multi-way file comparisons ]" << endl;
cout << " multiinter " << "Identifies common intervals among multiple interval files.\n";
cout << " unionbedg " << "Combines coverage intervals from multiple BEDGRAPH files.\n";
cout << endl;
cout << "[ Paired-end manipulation ]" << endl;
cout << " pairtobed " << "Find pairs that overlap intervals in various ways.\n";
cout << " pairtopair " << "Find pairs that overlap other pairs in various ways.\n";
cout << endl;
cout << "[ Format conversion ]" << endl;
cout << " bamtobed " << "Convert BAM alignments to BED (& other) formats.\n";
cout << " bedtobam " << "Convert intervals to BAM records.\n";
cout << " bamtofastq " << "Convert BAM records to FASTQ records.\n";
cout << " bedpetobam " << "Convert BEDPE intervals to BAM records.\n";
cout << " bed12tobed6 " << "Breaks BED12 intervals into discrete BED6 intervals.\n";
cout << endl;
cout << "[ Fasta manipulation ]" << endl;
cout << " getfasta " << "Use intervals to extract sequences from a FASTA file.\n";
cout << " maskfasta " << "Use intervals to mask sequences from a FASTA file.\n";
cout << " nuc " << "Profile the nucleotide content of intervals in a FASTA file.\n";
cout << endl;
cout << "[ BAM focused tools ]" << endl;
cout << " multicov " << "Counts coverage from multiple BAMs at specific intervals.\n";
cout << " tag " << "Tag BAM alignments based on overlaps with interval files.\n";
cout << endl;
cout << "[ Statistical relationships ]" << endl;
cout << " jaccard " << "Calculate the Jaccard statistic b/w two sets of intervals.\n";
cout << " reldist " << "Calculate the distribution of relative distances b/w two files.\n";
cout << endl;
cout << "[ Miscellaneous tools ]" << endl;
cout << " overlap " << "Computes the amount of overlap from two intervals.\n";
cout << " igv " << "Create an IGV snapshot batch script.\n";
cout << " links " << "Create a HTML page of links to UCSC locations.\n";
cout << " makewindows " << "Make interval \"windows\" across a genome.\n";
cout << " groupby " << "Group by common cols. & summarize oth. cols. (~ SQL \"groupBy\")\n";
cout << " expand " << "Replicate lines based on lists of values in columns.\n";
cout << endl;
cout << "[ General help ]" << endl;
cout << " --help " << "Print this help menu.\n";
//cout << " --faq " << "Frequently asked questions.\n"; TODO
cout << " --version " << "What version of bedtools are you using?.\n";
cout << " --contact " << "Feature requests, bugs, mailing lists, etc.\n";
cout << "\n";
return 0;
}
int bedtools_faq(void)
{
cout << "\n";
cout << "Q1. How do I see the help for a given command?" << endl;
cout << "A1. All BEDTools commands have a \"-h\" option. Additionally, some tools " << endl;
cout << " will provide the help menu if you just type the command line " << endl;
cout << " followed by enter. " << endl;
cout << "\n";
return 0;
}