/*
 * Copyright (c) 2013 Genome Research Ltd.
 * Author(s): James Bonfield
 * 
 * Redistribution and use in source and binary forms, with or without 
 * modification, are permitted provided that the following conditions are met:
 * 
 *    1. Redistributions of source code must retain the above copyright notice,
 *       this list of conditions and the following disclaimer.
 * 
 *    2. Redistributions in binary form must reproduce the above
 *       copyright notice, this list of conditions and the following
 *       disclaimer in the documentation and/or other materials provided
 *       with the distribution.
 * 
 *    3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
 *    Institute nor the names of its contributors may be used to endorse
 *    or promote products derived from this software without specific
 *    prior written permission.
 * 
 * THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS
 * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
 * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
 * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH
 * LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
 * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
 * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
 * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
 * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */

/*
 * A debugging program to dump out information on the layout of a CRAM file.
 * It's an abomination frankly, but isn't intended for production use.
 */

#ifdef HAVE_CONFIG_H
#include "io_lib_config.h"
#endif

#include <stdio.h>
#include <assert.h>
#include <ctype.h>
#include <string.h>
#include <limits.h>

#include <io_lib/cram.h>
#include <io_lib/zfio.h>

int main(int argc, char **argv) {
    cram_fd *fd;

    if (argc != 2 && argc != 3) {
	fprintf(stderr, "Usage: cram_index filename.cram [filename.cram.crai]\n");
	return 1;
    }

    if (NULL == (fd = cram_open(argv[1], "rb"))) {
	fprintf(stderr, "Error opening CRAM file '%s'.\n", argv[1]);
	return 1;
    }

    cram_set_option(fd, CRAM_OPT_REQUIRED_FIELDS,
		    SAM_RNAME | SAM_POS | SAM_CIGAR);

    if (cram_index_build(fd, argv[argc-1]) == -1) {
	cram_close(fd);
	return 1;
    }

    cram_close(fd);

    return 0;
}