#include "hdf5.h"
#include "hdf5_hl.h"
#include <stdlib.h>
#include <string.h>
#include <stdio.h>

#define SAMPLES 17
#define CHROMLEN 6
#define IDLEN 12
#define FILTERLEN 8
#define INFOLEN 30
#define FORMATLEN 30

#define NGENOFIELDS  (hsize_t)  9
#define NSITEFIELDS  (hsize_t)  9
#define NRECORDS (hsize_t)  6524
//define NRECORDS (hsize_t)  65248402



typedef struct Geno {
  int GT_0;
  int GT_1;
  int ATG;
  int MQ;
  int HCG;
  int GQ;
  int DP;
} Geno;

typedef struct Site{
  char chrom[CHROMLEN];
  int pos;
  char id[IDLEN];
  char ref;
  char alt;
  float qual;
  char filter[FILTERLEN];
  char info[INFOLEN];
  char format[FORMATLEN];
} Site;


int main(int argc, char *argv[]){
  if (argc<2){
	printf("no filename. %i args\n",argc);
	return -1;
  }
  Geno*  dst_buf=malloc(sizeof(Geno)*NRECORDS);
  /* Calculate the size and the offsets of our struct members in memory */
  size_t dst_size =  sizeof(Geno);
  size_t dst_offset[NGENOFIELDS] = { HOFFSET(Geno, GT_0 ),
				 HOFFSET(Geno, GT_1),
				 HOFFSET(Geno, ATG),
				 HOFFSET(Geno, MQ ),
				 HOFFSET(Geno, HCG ),
				 HOFFSET(Geno, GQ ),
				 HOFFSET(Geno, DP )

  };

  /* Define field information */
  const char *geno_field_names[NGENOFIELDS]  =    { "GT_0", "GT_1", "ATG", "MQ", "HCG", "GQ", "DP" };
  hid_t      geno_field_type[NGENOFIELDS];
  hid_t      file_id;
  hsize_t    chunk_size = 10;
  int        *fill_data = NULL;
  int        compress  = 0;
  herr_t     status;
  /* Initialize field_type */
  geno_field_type[0] = H5T_NATIVE_INT;
  geno_field_type[1] = H5T_NATIVE_INT;
  geno_field_type[2] = H5T_NATIVE_INT;
  geno_field_type[3] = H5T_NATIVE_INT;
  geno_field_type[4] = H5T_NATIVE_INT;
  geno_field_type[5] = H5T_NATIVE_INT;
  geno_field_type[6] = H5T_NATIVE_INT;



  /* Create a new file using default properties. */
  file_id = H5Fcreate( "strains17.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT );

  hid_t       group_id;  /* identifiers */
  /* Create a group */
  group_id = H5Gcreate(file_id, "/Genotypes", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);


  Site *  site_buf=malloc(sizeof(Site)*NRECORDS);
  /* Calculate the size and the offsets of our struct members in memory */
  size_t site_size =  sizeof(Site);

  
  /* Initialize field_type */
  hid_t string_chrom = H5Tcopy( H5T_C_S1 );
  H5Tset_size( string_chrom, CHROMLEN);

  hid_t string_id = H5Tcopy( H5T_C_S1 );
  H5Tset_size( string_id, IDLEN);

  hid_t string_filter = H5Tcopy( H5T_C_S1 );
  H5Tset_size( string_filter, FILTERLEN);

  hid_t string_info = H5Tcopy( H5T_C_S1 );
  H5Tset_size( string_info, INFOLEN);

  hid_t string_format = H5Tcopy( H5T_C_S1 );
  H5Tset_size( string_format, FORMATLEN);

  const char *site_field_names[NSITEFIELDS]  =    {"chrom","pos","id","ref","alt","qual","filter","info","format" };
  hid_t      site_field_type[NSITEFIELDS];

  site_field_type[0] = string_chrom;
  site_field_type[1] = H5T_NATIVE_INT;
  site_field_type[2] = string_id;
  site_field_type[3] = H5T_NATIVE_CHAR;
  site_field_type[4] = H5T_NATIVE_CHAR;
  site_field_type[5] = H5T_NATIVE_FLOAT;
  site_field_type[6] = string_filter;
  site_field_type[7] = string_info;
  site_field_type[8] = string_format;

  size_t site_offset[NSITEFIELDS] = { HOFFSET(Site, chrom ),
				      HOFFSET(Site, pos ),
				      HOFFSET(Site, id ),
				      HOFFSET(Site, ref ),
				      HOFFSET(Site, alt),
				      HOFFSET(Site, qual ),
				      HOFFSET(Site, filter ),
				      HOFFSET(Site, info ),
				      HOFFSET(Site, format ),
  };

  Site site;

  //array of array of genotypes
  Geno * genos[SAMPLES];
  int p;
  for (p=0; p<SAMPLES; p++){
    Geno *p_data=malloc(NRECORDS*sizeof(Site));    
    genos[p]=p_data;
  }

  char line[10000];      
  int j = 0;
  char * header[100];
  char headerline[10000];
  int numscanned; //number of site columns
  static Site site_data[NRECORDS];
  FILE *fp;
  if((fp=fopen(argv[1], "r"))==NULL) {
	printf("Cannot open file.\n");
	exit(1);
  }
  
  while(fgets(line, 10000, fp) && j < NRECORDS){
    printf ("%i\n", j);
	fflush(stdout);
    //check for comment
    line[strlen(line) - 1] = '\0';
    if (line[0] == '#'){
      //check if headerline
      if (line[1] == '#'){
	continue;
      } else {
	memcpy(headerline, line, sizeof(char) * strlen(line));
	char *thiscol = NULL;
	thiscol=strtok(headerline, "\t");
	thiscol=thiscol+1;
	int h = 0;
	while (thiscol != NULL ){
	  header[h] = thiscol;
	  printf("header %i: %s\n", h, header[h]);
	  h++;
	  thiscol = strtok(NULL, "\t");
	}

      }
      continue;
    }
    j++;

    //get columns describing site
    Site site;
    numscanned = sscanf(line, "%s %i %s %c %c %f %s %s %s" , site.chrom, &site.pos, site.id, &site.ref, &site.alt, &site.qual, site.filter, site.info, site.format);
    site_data[j]=site;

/*     printf ("quality is %f and filter is %s \n", site.qual, site.filter); */
/*     printf ("format is %s \n", site.format); */
    char * thisgenotype;
    thisgenotype=strtok(line, "\t");
    int i;

    //move past the site columns
    for (i = 0; i < numscanned - 1; i++){
      strtok(NULL, "\t");
    }

    //read the genotype columns
    for (i = 0; i < SAMPLES; i++){
      thisgenotype = strtok(NULL, "\t");
      Geno thisgeno;
      if (strncmp(thisgenotype, "./.", 3) == 0){
	//printf("no genotype \n");
	Geno geno = {-1, -1, -1, -1, -1, -1, -1};
	thisgeno = geno;
      } else {
	//printf("genotype %s \n", thisgenotype);
 sscanf(thisgenotype, "%i/%i:%i:%i:%i:%i:%i", &thisgeno.GT_0, &thisgeno.GT_1, &thisgeno.ATG, &thisgeno.MQ, &thisgeno.HCG, &thisgeno.GQ, &thisgeno.DP);
      }
      genos[i][j]=thisgeno;
    }
  }



  status=H5TBmake_table( "Site Data", group_id, "Sites", NSITEFIELDS, j,
			 site_size, site_field_names, site_offset, site_field_type,
			 chunk_size, fill_data, compress, site_data);
  int i;
  for (i=0; i<SAMPLES; i++){
    char tablename[30]="sample";
    //    printf("numscanned %i\n", numscanned);
    strcat(tablename, header[i+numscanned]);
    //printf ("table name %s\n", tablename);
    status=H5TBmake_table( tablename, group_id, tablename, NGENOFIELDS, j,
			   dst_size, geno_field_names, dst_offset, geno_field_type,
			   chunk_size, fill_data, compress, genos[i]);
  }  
  /*-------------------------------------------------------------------------
   * H5TBmake_table
   *-------------------------------------------------------------------------
   */





  /* Close the group. */
  status = H5Gclose(group_id);
  /* close the file */
  H5Fclose( file_id );
  return 0;
}