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Commit e55f9ecc authored by Aaron's avatar Aaron
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Uses C++ string comp. Thx to @jmarshall.

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src/bedtools.cpp
+ 39
− 43
View file @ e55f9ecc
......@@ -16,7 +16,6 @@
using namespace std;
// define our program name
#define PROGRAM_NAME "bedtools"
......@@ -63,8 +62,8 @@ int bedtools_faq(void);
/*
bedtools command line interface.
Thanks to Heng Li, as this interface is inspired and based upon his samtools interface.
Thanks to Heng Li, as this interface is inspired and
based upon his samtools interface.
*/
int main(int argc, char *argv[])
......@@ -72,56 +71,59 @@ 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 (strcmp(argv[1], "intersect") == 0) return intersect_main(argc-1, argv+1);
else if (strcmp(argv[1], "window") == 0) return window_main(argc-1, argv+1);
else if (strcmp(argv[1], "closest") == 0) return closest_main(argc-1, argv+1);
else if (strcmp(argv[1], "coverage") == 0) return coverage_main(argc-1, argv+1);
else if (strcmp(argv[1], "genomecov") == 0) return genomecoverage_main(argc-1, argv+1);
else if (strcmp(argv[1], "merge") == 0) return merge_main(argc-1, argv+1);
else if (strcmp(argv[1], "complement") == 0) return complement_main(argc-1, argv+1);
else if (strcmp(argv[1], "subtract") == 0) return subtract_main(argc-1, argv+1);
else if (strcmp(argv[1], "slop") == 0) return slop_main(argc-1, argv+1);
else if (strcmp(argv[1], "flank") == 0) return flank_main(argc-1, argv+1);
else if (strcmp(argv[1], "sort") == 0) return sort_main(argc-1, argv+1);
else if (strcmp(argv[1], "shuffle") == 0) return shuffle_main(argc-1, argv+1);
else if (strcmp(argv[1], "annotate") == 0) return annotate_main(argc-1, argv+1);
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 == "genomecov") return genomecoverage_main(argc-1, argv+1);
else if (sub_cmd == "merge") return merge_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 == "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 (strcmp(argv[1], "multiinter") == 0) return multiintersect_main(argc-1, argv+1);
else if (strcmp(argv[1], "unionbedg") == 0) return unionbedgraphs_main(argc-1, argv+1);
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 (strcmp(argv[1], "pairtobed") == 0) return pairtobed_main(argc-1, argv+1);
else if (strcmp(argv[1], "pairtopair") == 0) return pairtopair_main(argc-1, argv+1);
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 (strcmp(argv[1], "bamtobed") == 0) return bamtobed_main(argc-1, argv+1);
else if (strcmp(argv[1], "bedtobam") == 0) return bedtobam_main(argc-1, argv+1);
else if (strcmp(argv[1], "bedpetobam") == 0) return bedpetobam_main(argc-1, argv+1);
else if (strcmp(argv[1], "bed12tobed6") == 0) return bed12tobed6_main(argc-1, argv+1);
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 == "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 (strcmp(argv[1], "multicov") == 0) return multibamcov_main(argc-1, argv+1);
else if (strcmp(argv[1], "tag") == 0) return tagbam_main(argc-1, argv+1);
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 (strcmp(argv[1], "getfasta") == 0) return fastafrombed_main(argc-1, argv+1);
else if (strcmp(argv[1], "maskfasta") == 0) return maskfastafrombed_main(argc-1, argv+1);
else if (strcmp(argv[1], "nuc") == 0) return nuc_main(argc-1, argv+1);
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);
// misc. tools
else if (strcmp(argv[1], "overlap") == 0) return getoverlap_main(argc-1, argv+1);
else if (strcmp(argv[1], "igv") == 0) return bedtoigv_main(argc-1, argv+1);
else if (strcmp(argv[1], "links") == 0) return links_main(argc-1, argv+1);
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);
// help
else if (strcmp(argv[1], "-h") == 0) return bedtools_help();
else if (strcmp(argv[1], "--help") == 0) return bedtools_help();
else if (sub_cmd == "-h") return bedtools_help();
else if (sub_cmd == "--help") return bedtools_help();
else if (strcmp(argv[1], "FAQ") == 0) return bedtools_faq();
else if (sub_cmd == "FAQ") return bedtools_faq();
// unknown
else {
// TODO: Implement a Levenstein-based "did you mean???"
cerr << "error: unrecognized command: " << argv[1] << endl << endl;
return 1;
}
......@@ -190,18 +192,12 @@ int bedtools_help(void)
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 << "Q2. 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 1;
}
\ No newline at end of file
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