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Commit 54f37afb authored by arq5x's avatar arq5x
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merge conflict

parent df1de0db
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src/closestFile/closestHelp.cpp
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......@@ -99,137 +99,3 @@ void closest_help(void) {
// end the program here
exit(1);
}
=======
/*
* newClosestMain.cpp
*
* Created on: Sep 25, 2014
* Author: nek3d
*/
#include "closestFile.h"
#include "ContextClosest.h"
using namespace std;
// define our program name
#define PROGRAM_NAME "bedtools closest"
void closest_help(void);
int closest_main(int argc, char* argv[]) {
ContextClosest *context = new ContextClosest();
if (!context->parseCmdArgs(argc, argv, 1) || context->getShowHelp() || !context->isValidState()) {
if (!context->getErrorMsg().empty()) {
cerr << context->getErrorMsg() << endl;
}
closest_help();
delete context;
return 1;
}
ClosestFile *closestFile = new ClosestFile(context);
bool retVal = closestFile->getClosest();
delete closestFile;
delete context;
return retVal ? 0 : 1;
}
void closest_help(void) {
cerr << "\nTool: bedtools closest (aka closestBed)" << endl;
cerr << "Version: " << VERSION << "\n";
cerr << "Summary: For each feature in A, finds the closest " << endl;
cerr << "\t feature (upstream or downstream) in B." << endl << endl;
cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>" << endl << endl;
cerr << "Options: " << endl;
cerr << "\t-s\t" << "Req. same strandedness. That is, find the closest feature in" << endl;
cerr << "\t\tB that overlaps A on the _same_ strand." << endl;
cerr << "\t\t- By default, overlaps are reported without respect to strand." << endl << endl;
cerr << "\t-S\t" << "Req. opposite strandedness. That is, find the closest feature" << endl;
cerr << "\t\tin B that overlaps A on the _opposite_ strand." << endl;
cerr << "\t\t- By default, overlaps are reported without respect to strand." << endl << endl;
cerr << "\t-d\t" << "In addition to the closest feature in B, " << endl;
cerr << "\t\treport its distance to A as an extra column." << endl;
cerr << "\t\t- The reported distance for overlapping features will be 0." << endl << endl;
cerr << "\t-D\t" << "Like -d, report the closest feature in B, and its distance to A" << endl;
cerr << "\t\tas an extra column. Unlike -d, use negative distances to report" << endl;
cerr << "\t\tupstream features." << endl;
cerr << "\t\tThe options for defining which orientation is \"upstream\" are:" << endl;
cerr << "\t\t- \"ref\" Report distance with respect to the reference genome. " << endl;
cerr << "\t\t B features with a lower (start, stop) are upstream" << endl;
cerr << "\t\t- \"a\" Report distance with respect to A." << endl;
cerr << "\t\t When A is on the - strand, \"upstream\" means B has a" << endl;
cerr << "\t\t higher (start,stop)." << endl;
cerr << "\t\t- \"b\" Report distance with respect to B." << endl;
cerr << "\t\t When B is on the - strand, \"upstream\" means A has a" << endl;
cerr << "\t\t higher (start,stop)." << endl << endl;
cerr << "\t-io\t" << "Ignore features in B that overlap A. That is, we want close," << endl;
cerr << "\t\tyet not touching features only." << endl << endl;
cerr << "\t-iu\t" << "Ignore features in B that are upstream of features in A." << endl;
cerr << "\t\tThis option requires -D and follows its orientation" << endl;
cerr << "\t\trules for determining what is \"upstream\"." << endl << endl;
cerr << "\t-id\t" << "Ignore features in B that are downstream of features in A." << endl;
cerr << "\t\tThis option requires -D and follows its orientation" << endl;
cerr << "\t\trules for determining what is \"downstream\"." << endl << endl;
cerr << "\t-fu\t" << "Choose first from features in B that are upstream of features in A." << endl;
cerr << "\t\tThis option requires -D and follows its orientation" << endl;
cerr << "\t\trules for determining what is \"upstream\"." << endl << endl;
cerr << "\t-fd\t" << "Choose first from features in B that are downstream of features in A." << endl;
cerr << "\t\tThis option requires -D and follows its orientation" << endl;
cerr << "\t\trules for determining what is \"downstream\"." << endl << endl;
cerr << "\t-t\t" << "How ties for closest feature are handled. This occurs when two" << endl;
cerr << "\t\tfeatures in B have exactly the same \"closeness\" with A." << endl;
cerr << "\t\tBy default, all such features in B are reported." << endl;
cerr << "\t\tHere are all the options:" << endl;
cerr << "\t\t- \"all\" Report all ties (default)." << endl;
cerr << "\t\t- \"first\" Report the first tie that occurred in the B file." << endl;
cerr << "\t\t- \"last\" Report the last tie that occurred in the B file." << endl << endl;
cerr << "\t-mdb\t" << "How multiple databases are resolved." << endl;
cerr << "\t\t- \"each\" Report closest records for each database (default)." << endl;
cerr << "\t\t- \"all\" Report closest records among all databases." << endl << endl;
cerr << "\t-names\t" << "When using multiple databases (-b), provide an alias for each that" << endl;
cerr <<"\t\twill appear instead of a fileId when also printing the DB record." << endl << endl;
cerr << "\t-filenames" << "\tWhen using multiple databases (-b), show each complete filename" << endl;
cerr <<"\t\t\tinstead of a fileId when also printing the DB record." << endl << endl;
cerr << "\t-k\t" << "Report the k closest hits. Default is 1. If tieMode = \"all\", " << endl;
cerr << "\t\t- all ties will still be reported." << endl << endl;
cerr << "\t-N\t" << "Require that the query and the closest hit have different names." << endl;
cerr << "\t\tFor BED, the 4th column is compared." << endl << endl;
cerr << "\t-header\t" << "Print the header from the A file prior to results." << endl << endl;
cerr << "\t-nonamecheck\t" << "For sorted data, don't throw an error if the file has different naming conventions" << endl;
cerr << "\t\t\tfor the same chromosome. ex. \"chr1\" vs \"chr01\"." << endl << endl;
cerr << "Notes: " << endl;
cerr << "\tReports \"none\" for chrom and \"-1\" for all other fields when a feature" << endl;
cerr << "\tis not found in B on the same chromosome as the feature in A." << endl;
cerr << "\tE.g. none\t-1\t-1" << endl << endl;
// end the program here
exit(1);
}
>>>>>>> 7b280604de7e19a5c9af8340fd47ae892151415a:src/closestFile/closestMain.cpp
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