/*  File: glfMain.c
 *  Author: Richard Durbin (rd@sanger.ac.uk)
 *  Copyright (C) Genome Research Limited, 2008
 *-------------------------------------------------------------------
 * Description: main() for glf software
 * Exported functions:
 * HISTORY:
 * Last edited: Dec  9 17:53 2008 (rd)
 * Created: Fri Sep 19 15:01:50 2008 (rd)
 *-------------------------------------------------------------------
 */

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <assert.h>
#include <zlib.h>
#include "glf.h"

/*****************************************/

/* functions for adding likelihoods */

int qAddTable[1024] ;

static void qAddTableInit (void)
{
  int i ;
  for (i = 0 ; i < 1000 ; ++i)
    { double e = 1 + expPhred(i-512) ;
      qAddTable[i] = -logPhred(e) ;
    }
}

/*****************************************/

/* functions for scoring quality */

int qsumbit ;

int quality (glf3_t *g)
{ int k, q, qsum = 255, n0 = 0 ;

  /* use information that best (least) score is 0 */
  for (k = 0 ; k < 10 ; ++k)
    { if (g->lk[k]) qsum = qAdd (qsum, g->lk[k]) ;
      else ++n0 ;
    }
  qsumbit = -logPhred (n0 + expPhred(qsum)) ; /* recall that logPhred(x) is -10log_10(x), so this will be positive if non-zero */
  if (n0 == 1)
    q = qsum + qsumbit ;
  else
    q = logPhred ((n0-1+expPhred(qsum))) + qsumbit ;
  return q ;
}

/****************************************/

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

  --argc ; ++argv ;		/* remove program command */

  if (!argc || !strcmp (*argv, "-help") || !strcmp(*argv, "-h"))
    { fprintf (stderr, "Usage: glf <command> <options and arguments>\n") ;
      fprintf (stderr, "Commands:\n") ;
      fprintf (stderr, "  checkGenotype  check genotype\n") ;
      fprintf (stderr, "  soloPrior      apply prior for a single sequence\n") ;
      fprintf (stderr, "  trioPrior      apply prior for a mother/father/child trio\n") ;
      fprintf (stderr, "  snpCall        call SNPs from posterior odds glf (after applying a prior)\n") ;
      fprintf (stderr, "  subCall        call sites listed in a file from posterior odds glf\n") ;
      fprintf (stderr, "  dump           write out (a section of) glf file in text\n") ;
      fprintf (stderr, "  extract        extract a portion of a glf file into another file\n") ;
      fprintf (stderr, "  stats          information about the content of a glf file\n") ;
      fprintf (stderr, "  import         convert a glf dump to a glf\n") ;
      fprintf (stderr, "For specific help on any command type: glf <command> -help\n") ;
      exit (1) ;
    }

/*   if (!strcmp (*argv, "soloPrior")) */
/*     return glfSoloPrior (argc, argv) ; */
/*   else if (!strcmp (*argv, "trioPrior")) */
/*     return glfTrioPrior (argc, argv) ; */

  qAddTableInit();

  if (!strcmp (*argv, "dump"))
    return glfDump (argc, argv) ;
  else if (!strcmp (*argv, "extract"))
    return glfExtract (argc, argv) ;
  else if (!strcmp (*argv, "snpCall"))
    return glfSnpCall (argc, argv) ;
  else if (!strcmp (*argv, "soloPrior"))
    return glfSoloPrior (argc, argv) ;
  else if (!strcmp (*argv, "subCall"))
    return glfSubCall (argc, argv) ;
  else if (!strcmp (*argv, "stats"))
    return glfStats (argc, argv) ;
  else if (!strcmp (*argv, "checkGenotype"))
    return glfCheckGenotype (argc, argv) ;
  else if (!strcmp(*argv, "import"))
    return glfImport (argc,argv);

  fprintf (stderr, "Unknown command %s - type \"glf -help\" for help\n", *argv) ;
  exit (-1) ;
}

/************** end of file ************/