/*****************************************************************************
  mergeMain.cpp

  (c) 2009 - Aaron Quinlan
  Hall Laboratory
  Department of Biochemistry and Molecular Genetics
  University of Virginia
  aaronquinlan@gmail.com

  Licenced under the GNU General Public License 2.0 license.
******************************************************************************/
#include "mergeBed.h"
#include "version.h"

using namespace std;

// define our program name
#define PROGRAM_NAME "bedtools merge"


// define our parameter checking macro
#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)

// function declarations
void merge_help(void);

int merge_main(int argc, char* argv[]) {

    // our configuration variables
    bool showHelp = false;

    // input files
    string bedFile  = "stdin";
    int maxDistance = 0;
    string scoreOp  = "";

    // input arguments
    bool haveBed         = true;
    bool numEntries      = false;
    bool haveMaxDistance = false;
    bool forceStrand     = false;
    bool reportNames     = false;
    bool reportScores    = false;
    string delimiter     = ",";

    for(int i = 1; i < argc; i++) {
        int parameterLength = (int)strlen(argv[i]);

        if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
        (PARAMETER_CHECK("--help", 5, parameterLength))) {
            showHelp = true;
        }
    }

    if(showHelp) merge_help();

    // do some parsing (all of these parameters require 2 strings)
    for(int i = 1; i < argc; i++) {

        int parameterLength = (int)strlen(argv[i]);

        if(PARAMETER_CHECK("-i", 2, parameterLength)) {
            if ((i+1) < argc) {
                bedFile = argv[i + 1];
                i++;
            }
        }
        else if(PARAMETER_CHECK("-n", 2, parameterLength)) {
            numEntries = true;
        }
        else if(PARAMETER_CHECK("-d", 2, parameterLength)) {
            if ((i+1) < argc) {
                haveMaxDistance = true;
                maxDistance = atoi(argv[i + 1]);
                i++;
            }
        }
        else if (PARAMETER_CHECK("-s", 2, parameterLength)) {
            forceStrand = true;
        }
        else if (PARAMETER_CHECK("-nms", 4, parameterLength)) {
            reportNames = true;
        }
        else if (PARAMETER_CHECK("-scores", 7, parameterLength)) {
            reportScores = true;
            if ((i+1) < argc) {
                scoreOp      = argv[i + 1];
                i++;
            }
        }
        else if (PARAMETER_CHECK("-delim", 6, parameterLength)) {
            if ((i+1) < argc) {
                delimiter      = argv[i + 1];
                i++;
            }
        }
        else {
            cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
            showHelp = true;
        }
    }

    // make sure we have both input files
    if (!haveBed) {
        cerr << endl << "*****" << endl << "*****ERROR: Need -i BED file. " << endl << "*****" << endl;
        showHelp = true;
    }
    if ((reportScores == true) && (scoreOp != "sum")  
         && (scoreOp != "max")  && (scoreOp != "min") 
         && (scoreOp != "mean") && (scoreOp != "mode") 
         && (scoreOp != "median") && (scoreOp != "antimode") 
         && (scoreOp != "collapse")) 
    {
        cerr << endl 
             << "*****" 
             << endl 
             << "*****ERROR: Invalid scoreOp selection \"" 
             << scoreOp 
             << endl 
             << "\"  *****" 
             << endl;
        showHelp = true;
    }

    if (!showHelp) {
        BedMerge *bm = new BedMerge(bedFile, numEntries, 
                                    maxDistance, forceStrand, 
                                    reportNames, reportScores, 
                                    scoreOp, delimiter);
        delete bm;
    }
    else {
        merge_help();
    }
    return 0;
}

void merge_help(void) {
    
    cerr << "\nTool:    bedtools merge (aka mergeBed)" << endl;
    cerr << "Version: " << VERSION << "\n";        
    cerr << "Summary: Merges overlapping BED/GFF/VCF entries into a single interval." << endl << endl;

    cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf>" << endl << endl;

    cerr << "Options: " << endl;
    cerr << "\t-s\t"                     << "Force strandedness.  That is, only merge features" << endl;
    cerr                                 << "\t\tthat are the same strand." << endl;
    cerr                                 << "\t\t- By default, merging is done without respect to strand." << endl << endl;

    cerr << "\t-n\t"                     << "Report the number of BED entries that were merged." << endl;
    cerr                                 << "\t\t- Note: \"1\" is reported if no merging occurred." << endl << endl;


    cerr << "\t-d\t"                     << "Maximum distance between features allowed for features" << endl;
    cerr                                 << "\t\tto be merged." << endl;
    cerr                                 << "\t\t- Def. 0. That is, overlapping & book-ended features are merged." << endl;
    cerr                                 << "\t\t- (INTEGER)" << endl << endl;

    cerr << "\t-nms\t"                   << "Report the names of the merged features separated by commas." << endl;
    cerr                                 << "\t\tChange delim. with -delim." << endl << endl;
    
    cerr << "\t-scores\t"                << "Report the scores of the merged features. Specify one of " << endl;
    cerr                                 << "\t\tthe following options for reporting scores:" << endl;
    cerr                                 << "\t\t  sum, min, max," << endl;
    cerr                                 << "\t\t  mean, median, mode, antimode," << endl;
    cerr                                 << "\t\t  collapse (i.e., print a semicolon-separated list)," << endl;
    cerr                                 << "\t\t- (INTEGER)" << endl << endl;
    
    cerr << "\t-delim\t"                 << "Specify a custom delimiter for the -nms and -scores concat options" << endl;
    cerr                                 << "\t\t- Example: -delim \"|\"" << endl;
    cerr                                 << "\t\t- Default: \",\"." << endl << endl;
    
    
    cerr << "Notes: " << endl;
    cerr << "\t(1) All output, regardless of input type (e.g., GFF or VCF)" << endl;
    cerr << "\t    will in BED format with zero-based starts" << endl << endl;

    cerr << "\t(2) The input file (-i) file must be sorted by chrom, then start." << endl << endl;

    // end the program here
    exit(1);

}
