/*
 * main.c
 *
 * Copyright (c) 2008-2016 Ruibang Luo <aquaskyline.com>.
 *
 * This file is part of SOAPdenovo.
 *
 * SOAPdenovo is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * SOAPdenovo is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with SOAPdenovo.  If not, see <http://www.gnu.org/licenses/>.
 *
 */

#include "stdinc.h"
#include "newhash.h"
#include "kmerhash.h"
#include "extfunc.h"
#include "global.h"

extern int call_pregraph ( int arc, char **argv );
extern int call_pregraph_sparse(int arc, char **argv);
extern int call_heavygraph ( int arc, char **argv );
extern int call_map2contig ( int arc, char **argv );
extern int call_scaffold ( int arc, char **argv );
extern int call_align ( int arc, char **argv );

static void display_usage ();
static void display_all_usage ();
static void pipeline ( int argc, char **argv );

/*************************************************
Function:
    main
Description:
    The main function. It includes four modules:
    1.pregraph
    2.contig
    3.map
    4.scaffold
Input:
    @see display_all_usage ()
Output:
    Below files:
    1. *.contig
    2. *.scafSeq
    etc.
Return:
    None.
*************************************************/
int main ( int argc, char **argv )
{
  crc32c_Init();
  fprintf ( stderr, "\nVersion 2.04: released on July 13th, 2012\nCompile %s\t%s\n", __DATE__, __TIME__ );
  argc--;
  argv++;

  if ( argc == 0 )
    {
      display_usage ();
      return 0;
    }

  if ( strcmp ( "pregraph", argv[0] ) == 0 )
    {
      call_pregraph ( argc, argv );
    }
  else if(strcmp ( "sparse_pregraph", argv[0] ) == 0 )
    {
      call_pregraph_sparse ( argc, argv );

    }
  else if ( strcmp ( "contig", argv[0] ) == 0 )
    {
      call_heavygraph ( argc, argv );
    }
  else if ( strcmp ( "map", argv[0] ) == 0 )
    {
      call_align ( argc, argv );
    }
  //call_map2contig(argc,argv);
  else if ( strcmp ( "scaff", argv[0] ) == 0 )
    {
      call_scaffold ( argc, argv );
    }
  else if ( strcmp ( "all", argv[0] ) == 0 )
    {
      pipeline ( argc, argv );
    }
  else
    {
      display_usage ();
    }

  return 0;
}

static void display_usage ()
{
  fprintf ( stderr, "\nUsage: SOAPdenovo <command> [option]\n" );
  fprintf ( stderr, "    pregraph        construct kmer-graph\n" );
  fprintf ( stderr, "    sparse_pregraph construct sparse kmer-graph\n");
  fprintf ( stderr, "    contig          eliminate errors and output contigs\n" );
  fprintf ( stderr, "    map             map reads to contigs\n" );
  fprintf ( stderr, "    scaff           construct scaffolds\n" );
  fprintf ( stderr, "    all             do pregraph-contig-map-scaff in turn\n" );
}

static void pipeline ( int argc, char **argv )
{
  char *options[32];
  unsigned char getK, getRfile, getOfile, getD, getDD, getL, getR, getP, getF, getf, getk, getu, getG, getc, getC, getb, getB, getN, getw, getV;
  unsigned char getm, getE; //getr,
  char readfile[256], outfile[256];
  char temp[128];
  char *name;
  int kmer = 0, cutoff_len = 0, ncpu = 0, lowK = 0, lowC = 0, kmer_small = 0, gap_diff = 0, genome_size = 0;
  float min_cvg = 0.0, max_cvg = 0.0, insert_size_bound = 0.0, bubble_coverage = 0.0;
  char kmer_s[16], len_s[16], ncpu_s[16], M_s[16], lowK_s[16], lowC_s[16], kmer_small_s[16], gap_diff_s[16], min_cvg_s[16], max_cvg_s[16], insert_size_bound_s[16], bubble_coverage_s[16], genome_size_s[16];
  int i, copt, index, M = 1;
  int maxk;
  char maxk_s[16];
  char arcfilter_s[16];
  extern char *optarg;
  time_t start_t, stop_t;
  time ( &start_t );
  getK = getRfile = getOfile = getD = getDD = getL = getR = getP = getF = getf = getk = getu = getG =  getc = getC = getb = getB = getN = getw = getm = getE = getV = 0;

  while ( ( copt = getopt ( argc, argv, "a:s:o:K:M:L:p:G:d:D:RuFk:fc:C:b:B:N:wm:e:EV" ) ) != EOF ) //r
    {
      switch ( copt )
        {
        case 's':
          getRfile = 1;
          sscanf ( optarg, "%s", readfile );
          break;

        case 'o':
          getOfile = 1;
          sscanf ( optarg, "%s", outfile );
          break;

        case 'K':
          getK = 1;
          sscanf ( optarg, "%s", temp );
          kmer = atoi ( temp );
          break;

        case 'G':
          getG = 1;
          sscanf ( optarg, "%s", temp );
          gap_diff = atoi ( temp );
          break;

        case 'M':
          sscanf ( optarg, "%s", temp );
          M = atoi ( temp );
          break;

        case 'p':
          getP = 1;
          sscanf ( optarg, "%s", temp );
          ncpu = atoi ( temp );
          break;

        case 'L':
          getL = 1;
          sscanf ( optarg, "%s", temp );
          cutoff_len = atoi ( temp );
          break;

        case 'R':
          getR = 1;
          break;

        case 'u':
          getu = 1;
          maskRep = 0;
          break;

        case 'd':
          getD = 1;
          sscanf ( optarg, "%s", temp );
          lowK = atoi ( temp );
          break;

        case 'D':
          getDD = 1;
          sscanf ( optarg, "%s", temp );
          lowC = atoi ( temp );
          break;

        case 'a':
          initKmerSetSize = atoi ( optarg );
          break;

        case 'F':
          getF = 1;
          break;

        case 'k':
          getk = 1;
          sscanf ( optarg, "%s", temp );
          kmer_small = atoi ( temp );
          break;

        case 'f':
          getf = 1;
          break;

        case 'c':
          getc = 1;
          sscanf ( optarg, "%s", temp );
          min_cvg = atof ( temp );
          break;

        case 'C':
          getC = 1;
          sscanf ( optarg, "%s", temp );
          max_cvg = atof ( temp );
          break;

        case 'b':
          getb = 1;
          sscanf ( optarg, "%s", temp );
          insert_size_bound = atof ( temp );
          break;

        case 'B':
          getB = 1;
          sscanf ( optarg, "%s", temp );
          bubble_coverage = atof ( temp );
          break;

        case 'N':
          getN = 1;
          sscanf ( optarg, "%s", temp );
          genome_size = atoi ( temp );
          break;

        case 'w':
          getw = 1;
          break;

        case 'm':
          getm = 1;
          sscanf ( optarg, "%s", temp );
          maxk = atoi ( temp );
          break;

          /*
          case 'r':
          getr = 1;
          break;
          */
        case 'e':
          sscanf ( optarg, "%s", temp );
          arcfilter = atoi ( temp );
          break;

        case 'E':
          getE = 1;
          break;

        case 'V':
          getV = 1;
          break;

        default:

          if ( getRfile == 0 || getOfile == 0 )
            {
              display_all_usage ();
              exit ( -1 );
            }
        }
    }

  if ( getRfile == 0 || getOfile == 0 )
    {
      display_all_usage ();
      exit ( -1 );
    }

  if ( thrd_num < 1 )
    {
      thrd_num = 1;
    }

  // getK = getRfile = getOfile = getD = getL = getR = 0;
  name = "pregraph";
  index = 0;
  options[index++] = name;
  options[index++] = "-s";
  options[index++] = readfile;

  if ( getK )
    {
      options[index++] = "-K";
      sprintf ( kmer_s, "%d", kmer );
      options[index++] = kmer_s;
    }

  if ( getP )
    {
      options[index++] = "-p";
      sprintf ( ncpu_s, "%d", ncpu );
      options[index++] = ncpu_s;
    }

  if ( getD )
    {
      options[index++] = "-d";
      sprintf ( lowK_s, "%d", lowK );
      options[index++] = lowK_s;
    }

  if ( getR )
    {
      options[index++] = "-R";
    }

  options[index++] = "-o";
  options[index++] = outfile;
  /*
  for (i = 0; i < index; i++)
  {
      fprintf (stderr,"%s ", options[i]);
  }

  fprintf (stderr,"\n");
  */
  call_pregraph ( index, options );
  name = "contig";
  index = 0;
  options[index++] = name;
  options[index++] = "-g";
  options[index++] = outfile;
  options[index++] = "-M";
  sprintf ( M_s, "%d", M );
  options[index++] = M_s;

  if ( getR )
    {
      options[index++] = "-R";
    }

  if ( getDD )
    {
      options[index++] = "-D";
      sprintf ( lowC_s, "%d", lowC );
      options[index++] = lowC_s;
    }

  if ( getRfile )
    {
      options[index++] = "-s";
      options[index++] = readfile;
    }

  if ( getP )
    {
      options[index++] = "-p";
      sprintf ( ncpu_s, "%d", ncpu );
      options[index++] = ncpu_s;
    }

  if ( getm )
    {
      options[index++] = "-m";
      sprintf ( maxk_s, "%d", maxk );
      options[index++] = maxk_s;
    }

  /*
  if(getr){
      options[index++] = "-r";
  }
  */
  if ( getE )
    {
      options[index++] = "-E";
    }

  if ( arcfilter )
    {
      options[index++] = "-e";
      sprintf ( arcfilter_s, "%d", arcfilter );
      options[index++] = arcfilter_s;
    }

  /*
  for (i = 0; i < index; i++)
  {
      fprintf (stderr,"%s ", options[i]);
  }

  fprintf (stderr,"\n");
  */
  call_heavygraph ( index, options );
  name = "map";
  index = 0;
  options[index++] = name;
  options[index++] = "-s";
  options[index++] = readfile;
  options[index++] = "-g";
  options[index++] = outfile;

  if ( getP )
    {
      options[index++] = "-p";
      sprintf ( ncpu_s, "%d", ncpu );
      options[index++] = ncpu_s;
    }

  if ( getK )
    {
      options[index++] = "-K";
      sprintf ( kmer_s, "%d", kmer );
      options[index++] = kmer_s;
    }

  if ( getk )
    {
      options[index++] = "-k";
      sprintf ( kmer_small_s, "%d", kmer_small );
      options[index++] = kmer_small_s;
    }

  if ( getf )
    {
      options[index++] = "-f";
    }

  /*
  for (i = 0; i < index; i++)
  {
      fprintf (stderr,"%s ", options[i]);
  }

  fprintf (stderr,"\n");
  */
  call_align ( index, options );
  name = "scaff";
  index = 0;
  options[index++] = name;
  options[index++] = "-g";
  options[index++] = outfile;

  if ( getF )
    {
      options[index++] = "-F";
    }

  if ( getP )
    {
      options[index++] = "-p";
      sprintf ( ncpu_s, "%d", ncpu );
      options[index++] = ncpu_s;
    }

  if ( getL )
    {
      options[index++] = "-L";
      sprintf ( len_s, "%d", cutoff_len );
      options[index++] = len_s;
    }

  if ( getG )
    {
      options[index++] = "-G";
      sprintf ( gap_diff_s, "%d", gap_diff );
      options[index++] = gap_diff_s;
    }

  if ( getu )
    {
      options[index++] = "-u";
    }

  if ( getc )
    {
      options[index++] = "-c";
      sprintf ( min_cvg_s, "%f", min_cvg );
      options[index++] = min_cvg_s;
    }

  if ( getC )
    {
      options[index++] = "-C";
      sprintf ( max_cvg_s, "%f", max_cvg );
      options[index++] = max_cvg_s;
    }

  if ( getb )
    {
      options[index++] = "-b";
      sprintf ( insert_size_bound_s, "%f", insert_size_bound );
      options[index++] = insert_size_bound_s;
    }

  if ( getB )
    {
      options[index++] = "-B";
      sprintf ( bubble_coverage_s, "%f", bubble_coverage );
      options[index++] = bubble_coverage_s;
    }

  if ( getN )
    {
      options[index++] = "-N";
      sprintf ( genome_size_s, "%d", genome_size );
      options[index++] = genome_size_s;
    }

  if ( getw )
    {
      options[index++] = "-w";
    }

  if ( getV )
    {
      options[index++] = "-V";
    }

  /*
  for (i = 0; i < index; i++)
  {
      fprintf (stderr,"%s ", options[i]);
  }

  fprintf (stderr,"\n");
  */
  call_scaffold ( index, options );
  time ( &stop_t );
  fprintf ( stderr, "Time for the whole pipeline: %dm.\n", ( int ) ( stop_t - start_t ) / 60 );
}

static void display_all_usage ()
{
  //  fprintf (stderr,"\nSOAPdenovo all -s configFile -o outputGraph [-R -f -F -u -w] [-K kmer -p n_cpu -a initMemoryAssumption -d KmerFreqCutOff -D EdgeCovCutoff -M mergeLevel -k kmer_R2C, -G gapLenDiff -L minContigLen -c minContigCvg -C maxContigCvg -b insertSizeUpperBound -B bubbleCoverage -N genomeSize]\n");
  fprintf ( stderr, "\nSOAPdenovo all -s configFile -o outputGraph [-R -F -u -w] [-K kmer -p n_cpu -a initMemoryAssumption -d KmerFreqCutOff -D EdgeCovCutoff -M mergeLevel -k kmer_R2C, -G gapLenDiff -L minContigLen -c minContigCvg -C maxContigCvg -b insertSizeUpperBound -B bubbleCoverage -N genomeSize]\n" );
  fprintf ( stderr, "  -s <string>    configFile: the config file of solexa reads\n" );
  fprintf ( stderr, "  -o <string>    outputGraph: prefix of output graph file name\n" );
#ifdef MER127
  fprintf ( stderr, "  -K <int>       kmer(min 13, max 127): kmer size, [23]\n" );
#else
  fprintf ( stderr, "  -K <int>       kmer(min 13, max 63): kmer size, [23]\n" );
#endif
  fprintf ( stderr, "  -p <int>       n_cpu: number of cpu for use, [8]\n" );
  fprintf ( stderr, "  -a <int>       initMemoryAssumption: memory assumption initialized to avoid further reallocation, unit G, [0]\n" );
  fprintf ( stderr, "  -d <int>       kmerFreqCutoff: kmers with frequency no larger than KmerFreqCutoff will be deleted, [0]\n" );
  fprintf ( stderr, "  -R (optional)  resolve repeats by reads, [NO]\n" );
  fprintf ( stderr, "  -D <int>       edgeCovCutoff: edges with coverage no larger than EdgeCovCutoff will be deleted, [1]\n" );
  fprintf ( stderr, "  -M <int>       mergeLevel(min 0, max 3): the strength of merging similar sequences during contiging, [1]\n" );
  fprintf ( stderr, "  -e <int>       arcWeight: two edges, between which the arc's weight is larger than arcWeight, will be linerized, [0]\n" );
#ifdef MER127
  fprintf ( stderr, "  -m <int>       maxKmer (max 127): maximum kmer size used for multi-kmer, [NO]\n" );
#else
  fprintf ( stderr, "  -m <int>       maxKmer (max 63): maximum kmer size used for multi-kmer, [NO]\n" );
#endif
  fprintf ( stderr, "  -E (optional)  merge clean bubble before iterate, works only if -M is set when using multi-kmer, [NO]\n" );
  //  printf ("  -O (optional)\toutput contig of each kmer when iterating\n");
  //  fprintf (stderr,"  -f (optional)  output gap related reads in map step for using SRkgf to fill gaps, [NO]\n");
#ifdef MER127
  fprintf ( stderr, "  -k <int>       kmer_R2C(min 13, max 127): kmer size used for mapping reads to contigs, [K]\n" );
#else
  fprintf ( stderr, "  -k <int>       kmer_R2C(min 13, max 63): kmer size used for mapping reads to contigs, [K]\n" );
#endif
  fprintf ( stderr, "  -F (optional)  fill gaps in scaffolds, [NO]\n" );
  fprintf ( stderr, "  -u (optional)  un-mask contigs with high/low coverage before scaffolding, [mask]\n" );
  fprintf ( stderr, "  -w (optional)  keep contigs weakly connected to other contigs in scaffold, [NO]\n" );
  fprintf ( stderr, "  -G <int>       gapLenDiff: allowed length difference between estimated and filled gap, [50]\n" );
  fprintf ( stderr, "  -L <int>       minContigLen: shortest contig for scaffolding, [K+2]\n" );
  fprintf ( stderr, "  -c <float>     minContigCvg: minimum contig coverage (c*avgCvg), contigs shorter than 100bp with coverage smaller than c*avgCvg will be masked before scaffolding unless -u is set, [0.1]\n" );
  fprintf ( stderr, "  -C <float>     maxContigCvg: maximum contig coverage (C*avgCvg), contigs with coverage larger than C*avgCvg or contigs shorter than 100bp with coverage larger than 0.8*C*avgCvg will be masked before scaffolding unless -u is set, [2]\n" );
  fprintf ( stderr, "  -b <float>     insertSizeUpperBound: (b*avg_ins) will be used as upper bound of insert size for large insert size ( > 1000) when handling pair-end connections between contigs if b is set to larger than 1, [1.5]\n" );
  fprintf ( stderr, "  -B <float>     bubbleCoverage: remove contig with lower cvoerage in bubble structure if both contigs' coverage are smaller than bubbleCoverage*avgCvg, [0.6]\n" );
  fprintf ( stderr, "  -N <int>       genomeSize: genome size for statistics, [0]\n" );
  fprintf ( stderr, "  -V (optional)  output information for Hawkeye to visualize the assembly, [NO]\n" );
}