/*****************************************************************************
  pairToBedMain.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 "pairToBed.h"
#include "version.h"

using namespace std;

// define our program name
#define PROGRAM_NAME "pairToBed"

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

// function declarations
void ShowHelp(void);

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

    // our configuration variables
    bool showHelp = false;

    // input files
    string bedAFile;
    string bedBFile;

    // input arguments
    float overlapFraction = 1E-9;
    string searchType = "either";

    // flags to track parameters
    bool haveBedA           = false;
    bool haveBedB           = false;
    bool haveSearchType     = false;
    bool haveFraction       = false;
    bool sameStrand         = false;
    bool diffStrand         = false;
    bool useEditDistance    = false;
    bool inputIsBam         = false;
    bool outputIsBam        = true;
    bool uncompressedBam    = false;

    // check to see if we should print out some help
    if(argc <= 1) showHelp = true;

    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) ShowHelp();

    // 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("-a", 2, parameterLength)) {
            if ((i+1) < argc) {
                haveBedA = true;
                outputIsBam  = false;
                bedAFile = argv[i + 1];
                i++;
            }
        }
        else if(PARAMETER_CHECK("-abam", 5, parameterLength)) {
            if ((i+1) < argc) {
                haveBedA = true;
                inputIsBam = true;
                bedAFile = argv[i + 1];
                i++;
            }
        }
        else if(PARAMETER_CHECK("-b", 2, parameterLength)) {
            if ((i+1) < argc) {
                haveBedB = true;
                bedBFile = argv[i + 1];
                i++;
            }
        }
        else if(PARAMETER_CHECK("-bedpe", 6, parameterLength)) {
            outputIsBam = false;
        }
        else if(PARAMETER_CHECK("-ed", 3, parameterLength)) {
            useEditDistance = true;
        }
        else if(PARAMETER_CHECK("-type", 5, parameterLength)) {
            if ((i+1) < argc) {
                haveSearchType = true;
                searchType = argv[i + 1];
                i++;
            }
        }
        else if(PARAMETER_CHECK("-f", 2, parameterLength)) {
            if ((i+1) < argc) {
                haveFraction = true;
                overlapFraction = atof(argv[i + 1]);
                i++;
            }
        }
        else if (PARAMETER_CHECK("-s", 2, parameterLength)) {
            sameStrand = true;
        }
        else if (PARAMETER_CHECK("-S", 2, parameterLength)) {
            diffStrand = true;
        }
        else if(PARAMETER_CHECK("-ubam", 5, parameterLength)) {
            uncompressedBam = true;
        }
        else {
            cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
            showHelp = true;
        }
    }


    // make sure we have both input files
    if (!haveBedA || !haveBedB) {
        cerr << endl << "*****" << endl << "*****ERROR: Need -a and -b files. " << endl << "*****" << endl;
        showHelp = true;
    }

    if (haveSearchType && (searchType != "either") && (searchType != "neither") && (searchType != "both")
                        && (searchType != "xor") && (searchType != "notboth") && (searchType != "ispan")
                        && (searchType != "ospan") && (searchType != "notispan") && (searchType != "notospan")) {
        cerr << endl << "*****" << endl << "*****ERROR: Request \"either\" or \"both\" or \"neither\" or \"xor\" or \"notboth\" or \"ispan\" or \"ospan\" or \"notispan\" or \"notospan\"" << endl << "*****" << endl;
        showHelp = true;
    }

    if ( ((searchType == "ispan") || (searchType == "ospan") || (searchType == "notispan") || (searchType == "notospan"))
         && (sameStrand || diffStrand) ) {
        cerr << endl << "*****" << endl << "*****ERROR: Cannot enforce strandedness with selected searchtype" << endl << "*****" << endl;
        showHelp = true;
    }

    if (useEditDistance && (inputIsBam == false || outputIsBam == true)) {
        cerr << endl << "*****" << endl << "*****ERROR: -ed must be used with -bedpe and -abam." << endl << "*****" << endl;
        showHelp = true;
    }
    
    if (sameStrand && diffStrand) {
        cerr << endl << "*****" << endl << "*****ERROR: Request either -s OR -S, not both." << endl << "*****" << endl;
        showHelp = true;
    }
    if (!showHelp) {

        BedIntersectPE *bi = new BedIntersectPE(bedAFile, bedBFile, overlapFraction,
                                                searchType, sameStrand, diffStrand, inputIsBam,
                                                outputIsBam, uncompressedBam, useEditDistance);
        delete bi;
        return 0;
    }
    else {
        ShowHelp();
    }
}


void ShowHelp(void) {

    cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;

    cerr << "Author:  Aaron Quinlan (aaronquinlan@gmail.com)" << endl;

    cerr << "Summary: Report overlaps between a BEDPE file and a BED/GFF/VCF file." << endl << endl;

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

    cerr << "Options: " << endl;

    cerr << "\t-abam\t"         << "The A input file is in BAM format.  Output will be BAM as well." << endl;
    cerr                        << "\t\t- Requires BAM to be grouped or sorted by query." << endl << endl;

    cerr << "\t-ubam\t"         << "Write uncompressed BAM output. Default is to write compressed BAM." << endl << endl;
    cerr                        << "\t\tis to write output in BAM when using -abam." << endl << endl;

    cerr << "\t-bedpe\t"        << "When using BAM input (-abam), write output as BEDPE. The default" << endl;
    cerr                        << "\t\tis to write output in BAM when using -abam." << endl << endl;

    cerr << "\t-ed\t"           << "Use BAM total edit distance (NM tag) for BEDPE score." << endl;
    cerr                        << "\t\t- Default for BEDPE is to use the minimum of" << endl;
    cerr                        << "\t\t  of the two mapping qualities for the pair." << endl;
    cerr                        << "\t\t- When -ed is used the total edit distance" << endl;
    cerr                        << "\t\t  from the two mates is reported as the score." << endl << endl;

    cerr << "\t-f\t"                    << "Minimum overlap required as fraction of A (e.g. 0.05)." << endl;
    cerr                                << "\t\tDefault is 1E-9 (effectively 1bp)." << endl << endl;

    cerr << "\t-s\t"                    << "Require same strandedness when finding overlaps." << endl;
    cerr                                << "\t\tDefault is to ignore stand." << endl;
    cerr                                << "\t\tNot applicable with -type inspan or -type outspan." << endl << endl;

    cerr << "\t-S\t"                    << "Require different strandedness when finding overlaps." << endl;
    cerr                                << "\t\tDefault is to ignore stand." << endl;
    cerr                                << "\t\tNot applicable with -type inspan or -type outspan." << endl << endl;

    cerr << "\t-type \t"                << "Approach to reporting overlaps between BEDPE and BED." << endl << endl;
    cerr                                << "\t\teither\tReport overlaps if either end of A overlaps B." << endl;
    cerr                                    << "\t\t\t- Default." << endl;

    cerr                                << "\t\tneither\tReport A if neither end of A overlaps B." << endl;

    cerr                                << "\t\tboth\tReport overlaps if both ends of A overlap  B." << endl;

    cerr                                << "\t\txor\tReport overlaps if one and only one end of A overlaps B." << endl;

    cerr                                << "\t\tnotboth\tReport overlaps if neither end or one and only one " << endl;
    cerr                                    << "\t\t\tend of A overlap B.  That is, xor + neither." << endl << endl;

    cerr                                << "\t\tispan\tReport overlaps between [end1, start2] of A and B." << endl;
    cerr                                    << "\t\t\t- Note: If chrom1 <> chrom2, entry is ignored." << endl << endl;

    cerr                                << "\t\tospan\tReport overlaps between [start1, end2] of A and B." << endl;
    cerr                                    << "\t\t\t- Note: If chrom1 <> chrom2, entry is ignored." << endl << endl;

    cerr                                << "\t\tnotispan\tReport A if ispan of A doesn't overlap B." << endl;
    cerr                                    << "\t\t\t\t- Note: If chrom1 <> chrom2, entry is ignored." << endl << endl;

    cerr                                << "\t\tnotospan\tReport A if ospan of A doesn't overlap B." << endl;
    cerr                                    << "\t\t\t\t- Note: If chrom1 <> chrom2, entry is ignored." << endl << endl;

    cerr << "Refer to the BEDTools manual for BEDPE format." << endl << endl;

    exit(1);
}