/*
 * contig.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 "extvab.h"
static void initenv ( int argc, char **argv );
static void display_contig_usage ();
char shortrdsfile[256], graphfile[256];
static boolean repeatSolve;     //whether solve repeat or not
//static boolean keepReadFile = 0;  //whether keep tmp selected reads file or not
static boolean iter = 0;                //whether use multikmer or not
static boolean cleanBubble = 0;     //whether merge clean bubble before iterate
static int M = 1;           //merge bubble level
static int maxk = 0;        //max kmer of multikmer

/*************************************************
Function:
    call_heavygraph
Description:
    The main function for contig step . its processes are as below:
    1. Solve repeat
    2. Merge bubble(clean bubble is optional for multikmer)
    3. Remove weak edge and low coverage edge
    4. Cut tips
    5. Iterate multikmer(optional)
Input:
    @see display_contig_usage ()
Output:
    The files below:
    1. *.contig
    2. *.ContigIndex
    3. *.update.edge
    4. *.Arc
    5. *.read           [optional]
    6. *.preGraphBasic  [optional]
Return:
    None.
*************************************************/
int call_heavygraph ( int argc, char **argv )
{
  time_t start_t, stop_t, time_bef, time_aft;
  time ( &start_t );
  boolean ret;
  fprintf ( stderr, "\n********************\n" );
  fprintf ( stderr, "Contig\n" );
  fprintf ( stderr, "********************\n\n" );
  initenv ( argc, argv );
  loadVertex ( graphfile );
  loadEdge ( graphfile );

  if ( repeatSolve )
    {
      ret = loadPathBin ( graphfile );
    }

  swapedge();
  sortedge();
  freshArc();

  if ( repeatSolve )
    {
      time ( &time_bef );

      //      ret = loadPathBin (graphfile);
      if ( ret )
        {
          solveReps ();
        }
      else
        {
          fprintf ( stderr, "Repeat solving can't be done...\n" );
        }

      time ( &time_aft );
      fprintf ( stderr, "Time spent on solving repeat: %ds.\n", ( int ) ( time_aft - time_bef ) );
    }

  //edgecvg_bar(edge_array,num_ed,graphfile,100);

  if ( !iter && M > 0 )
    {
      time ( &time_bef );
      bubblePinch ( 0.90, graphfile, M, 0, 1 );
      time ( &time_aft );
      fprintf ( stderr, "Time spent on pinching bubbles: %ds.\n", ( int ) ( time_aft - time_bef ) );
    }

  if ( iter && cleanBubble && M > 0 )
    {
      time ( &time_bef );
      clean = 1;
      long long oldpinCounter = 0;
      long long min = 10;
      int times = 0;

      while ( min >= 10 )
        {
          times++;

          if ( times >= 4 )
            {
              break;
            }

          bubblePinch ( 0.90, graphfile, M, 1, 0 );
          min = pinCounter;
          fprintf ( stderr, "%lld clean bubbles merged.\n", pinCounter );
        }

      time ( &time_aft );
      fprintf ( stderr, "Time spent on pinching clean bubbles: %ds.\n", ( int ) ( time_aft - time_bef ) );
      clean = 0;
    }

  if ( deLowEdge )
    {
      removeWeakEdges ( 2 * overlaplen, 1 );
      removeLowCovEdges ( 2 * overlaplen, deLowEdge, !iter );
    }

  cutTipsInGraph ( 0, 0, !iter );

  if ( iter )
    {
      Iterate ( shortrdsfile, graphfile, maxk, M ); //keepReadFile,

      if ( M > 0 )
        {
          time ( &time_bef );
          bubblePinch ( 0.90, graphfile, M, 1, 0 );
          time ( &time_aft );
          fprintf ( stderr, "Time spent on pinching bubbles: %ds.\n", ( int ) ( time_aft - time_bef ) );
        }

      freshpreGraphBasic ( iter, maxk, graphfile );
    }

  //output_graph(graphfile);
  output_contig ( edge_array, num_ed, graphfile, overlaplen + 1 );
  output_updated_edges ( graphfile );
  output_heavyArcs ( graphfile );

  if ( vt_array )
    {
      free ( ( void * ) vt_array );
      vt_array = NULL;
    }

  if ( edge_array )
    {
      free_edge_array ( edge_array, num_ed_limit );
      edge_array = NULL;
    }

  destroyArcMem ();
  time ( &stop_t );
  fprintf ( stderr, "\nTime spent on constructing contig: %dm.\n\n", ( int ) ( stop_t - start_t ) / 60 );
  return 0;
}


/*****************************************************************************
 * Parse command line switches
 *****************************************************************************/
void initenv ( int argc, char **argv )
{
  int copt;
  int inpseq, outseq;
  extern char *optarg;
  char temp[100];
  inpseq = outseq = repeatSolve = iter = cleanBubble = 0;//keepReadFile =
  optind = 1;
  fprintf ( stderr, "Parameters: contig " );

  while ( ( copt = getopt ( argc, argv, "g:M:D:Rs:m:p:e:E" ) ) != EOF ) // r
    {
      switch ( copt )
        {
        case 'M':
          fprintf ( stderr, "-M %s ", optarg );
          sscanf ( optarg, "%s", temp );
          M = atoi ( temp );
          break;

        case 'D':
          fprintf ( stderr, "-D %s ", optarg );
          sscanf ( optarg, "%s", temp );
          deLowEdge = atoi ( temp ) >= 0 ? atoi ( temp ) : 0;
          break;

        case 'g':
          fprintf ( stderr, "-g %s ", optarg );
          inGraph = 1;
          sscanf ( optarg, "%s", graphfile );
          break;

        case 'R':
          repeatSolve = 1;
          fprintf ( stderr, "-R " );
          break;

        case 's':
          fprintf ( stderr, "-s %s ", optarg );
          inpseq = 1;
          sscanf ( optarg, "%s", shortrdsfile );
          break;

        case 'm':
          fprintf ( stderr, "-m %s ", optarg );
          iter = 1;
          sscanf ( optarg, "%s", temp );
          maxk = atoi ( temp );
          break;

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

        case 'p':
          fprintf ( stderr, "-p %s ", optarg );
          sscanf ( optarg, "%s", temp );
          thrd_num = atoi ( temp );
          break;

        case 'E':
          cleanBubble = 1;
          fprintf ( stderr, "-E " );
          break;

        default:

          if ( ( iter && inpseq == 0 ) || inGraph == 0 )
            {
              display_contig_usage ();
              exit ( -1 );
            }
        }
    }

  fprintf ( stderr, "\n\n" );

  if ( iter )
    {
      if ( maxk % 2 == 0 )
        {
          maxk++;
          fprintf ( stderr, "Max K should be an odd number, change to %d.\n", maxk );
        }

      if ( maxk < 13 )
        {
          maxk = 13;
          fprintf ( stderr, "Max K should not be less than 13, change to %d.\n", maxk );
        }

#ifdef MER127
      else if ( maxk > 127 )
        {
          maxk = 127;
          fprintf ( stderr, "Max K should not be greater than 127, change to %d.\n", maxk );
        }

#else
      else if ( maxk > 63 )
        {
          maxk = 63;
          fprintf ( stderr, "Max K should not be greater than 63, change to %d.\n", maxk );
        }

#endif

      if ( maxk <= overlaplen )
        {
          fprintf ( stderr, "Max K %d is not greater than overlaplen %d.\n", maxk, overlaplen );
          display_contig_usage ();
          exit ( -1 );
        }
    }

  if ( ( iter && inpseq == 0 ) || inGraph == 0 )
    {
      display_contig_usage ();
      exit ( -1 );
    }
}

static void display_contig_usage ()
{
  fprintf ( stderr, "\ncontig -g InputGraph [-R] [-M mergeLevel -D EdgeCovCutoff] [-s readsInfoFile -m maxkmer -p n_cpu -r]\n" );
  fprintf ( stderr, "  -g <string>      inputGraph: prefix of input graph file names\n" );
  fprintf ( stderr, "  -R (optional)    resolve repeats using information generated in pregraph step, works only if -R is set in pregraph step too, [NO]\n" );
  fprintf ( stderr, "  -M <int>         mergeLevel(min 0, max 3): the strength of merging similar sequences during contiging, [1]\n" );
  fprintf ( stderr, "  -D <int>         EdgeCovCutoff: edges shorter than (2*K+1) with coverage no larger than EdgeCovCutoff will be deleted, [1]\n" );
  fprintf ( stderr, "  -e <int>         arcWeight: two edges, between which the arc's weight is larger than arcWeight, will be linerized, [0]\n" );
  fprintf ( stderr, "  -m <int>         max k when using multi-kmer, and the parameters below are used along with multi-kmer, [NO]\n" );
  fprintf ( stderr, "      -s <string>      readsInfoFile:The file contains information of solexa reads(It's necessary when using multi-kmer)\n" );
  fprintf ( stderr, "      -p <int>         number of cpu, [8]\n" );
  fprintf ( stderr, "      -E (optional)    merge clean bubble before iterate, works only if -M is set when using multi-kmer, [NO]\n" );
  //  fprintf (stderr,"  -r (optional)    keep available read(*.read)\n");
}