taf_index.c

/*
 * taf_index: Make a .tai index from a TAF or MAF file (which can be bgzipped or uncompressed)
 *
 *  Released under the MIT license, see LICENSE.txt
*/

#include "taf.h"
#include "tai.h"
#include <getopt.h>
#include <time.h>

static void usage(void) {
    fprintf(stderr, "taffy index [options]\n");
    fprintf(stderr, "Index a TAF or MAF file, output goes in <file>.tai\n");
    fprintf(stderr, "-i --inputFile : Input taf or maf file [REQUIRED]\n");
    fprintf(stderr, "-b --blockSize : Write an index line for intervals of this many bp [default:10000]\n");
    fprintf(stderr, "-l --logLevel : Set the log level\n");
    fprintf(stderr, "-h --help : Print this help message\n");
}

int taf_index_main(int argc, char *argv[]) {
    time_t startTime = time(NULL);

    /*
     * Arguments/options
     */
    char *logLevelString = NULL;
    char *taf_fn = NULL;
    int64_t block_size = 10000;

    ///////////////////////////////////////////////////////////////////////////
    // Parse the inputs
    ///////////////////////////////////////////////////////////////////////////

    while (1) {
        static struct option long_options[] = { { "logLevel", required_argument, 0, 'l' },
                                                { "inputFile", required_argument, 0, 'i' },
                                                { "blockSize", required_argument, 0, 'b' },
                                                { "help", no_argument, 0, 'h' },
                                                { 0, 0, 0, 0 } };

        int option_index = 0;
        int64_t key = getopt_long(argc, argv, "l:i:b:h", long_options, &option_index);
        if (key == -1) {
            break;
        }

        switch (key) {
            case 'l':
                logLevelString = optarg;
                break;
            case 'i':
                taf_fn = optarg;
                break;
            case 'b':
                block_size = atoi(optarg);
                break;
            case 'h':
                usage();
                return 0;
            default:
                usage();
                return 1;
        }
    }

    //////////////////////////////////////////////
    //Log the inputs
    //////////////////////////////////////////////

    st_setLogLevelFromString(logLevelString);
    st_logInfo("Input file string : %s\n", taf_fn);
    st_logInfo("Block size : %" PRIi64 "\n", block_size);
    
    //////////////////////////////////////////////
    // Make the .tai index
    //////////////////////////////////////////////

    if (taf_fn == NULL) {
        fprintf(stderr, "Input file must be specified with -i\n");
        return 1;        
    }
    FILE *taf_fh = fopen(taf_fn, "r");
    if (taf_fh == NULL) {
        fprintf(stderr, "Unable to open input file: %s\n", taf_fn);
        return 1;
    }
    char *tai_fn = tai_path(taf_fn);
    st_logInfo("Output index file : %s\n", tai_fn);
    FILE *tai_fh = fopen(tai_fn, "w");    
    LI *li = LI_construct(taf_fh);
    if (!LI_indexable(li)) {
        fprintf(stderr, "Input file must be either uncompressed or bgzipped: gzip not supported: %s\n", taf_fn);
        return 1;
    }

    tai_create(li, tai_fh, block_size);

    //////////////////////////////////////////////
    // Cleanup
    //////////////////////////////////////////////

    if(taf_fh != NULL) {
        fclose(taf_fh);
    }
    if(tai_fh != NULL) {
        fclose(tai_fh);
    }
    free(tai_fn);

    LI_destruct(li);
    
    st_logInfo("taffy index is done, %" PRIi64 " seconds have elapsed\n", time(NULL) - startTime);

    return 0;
}