/*  File: glfDump.c
 *  Author: Richard Durbin (rd@sanger.ac.uk)
 *  Copyright (C) Genome Research Limited, 2008
 *-------------------------------------------------------------------
 * Description: Prints out information in a .glf file as a text file
 * Exported functions: glfDump
 * HISTORY:
 * Last edited: May 4 15:33 2008 (lj4@sanger.ac.uk)
 * * April 30 15:24 2009 (lj4@sanger.ac.uk): updated code to handle GLF version 3 files  
 * Created: Wed Sep  3 09:35:40 2008 (rd)
 *-------------------------------------------------------------------
 */

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <stdint.h>
#include "glf.h"
#include "bgzf.h"

static char *NAME = 0 ;
static int START = 1 ;
static int END = 1000000000 ;

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

  glfFile fpIn ; 
  glf3_header_t *h;
  char *name;
  glf3_t *g3;
  int len;

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

  while (argc)
    if (!strcmp(argv[0], "-name") && argc >= 2)
      { NAME = argv[1] ; argc -= 2 ; argv += 2 ; }
    else if (!strcmp (argv[0], "-start") && argc >= 2)
      { START = atoi(argv[1]) ; argc -= 2 ; argv += 2 ; }
    else if (!strcmp (argv[0], "-end") && argc >= 2)
      { END = atoi(argv[1]) ; argc -= 2 ; argv += 2 ; }
    else
      { fprintf (stderr, "Usage: glf dump [-start xx] [-end yy] < x.glf > x.txt // makes a text version of the GLF file\n") ; return 1 ; }

  if (!(fpIn = bgzf_fdopen(fileno(stdin), "r")))
    { fprintf (stderr, "failed to open stdin as .glz file\n") ; return 1 ; }

  --START ;

  /* initialise glf3 objects */
  h = glf3_header_read(fpIn);
  g3 = glf3_init1();

  while ((name = glf3_ref_read(fpIn, &len)) != 0) {
    int pos = 0;
    fprintf(stderr,"%s\n",name);
    while (glf3_read1(fpIn, g3) && g3->rtype != GLF3_RTYPE_END) {
      pos += g3->offset;

      if (pos >= START && pos < END && (!NAME || !strcmp(NAME, name)))
	glf3_view1(name, g3, pos);
    }
    free(name);
  }

  /* clean everything up */
  glf3_header_destroy(h);
  glf3_destroy1(g3);
  bgzf_close(fpIn);

  return 0 ;
}

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