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GH/Sim4/sim4.2002-03-03/sim4b1.c  view on Meta::CPAN

};

#define HASH_SIZE 32767        /* 2**15 - 1 */
#define GEN_LOG4_ENTRIES 45
#define CDNA_LOG4_ENTRIES 25
static struct hash_node *phashtab[HASH_SIZE+1];
static struct hash_node **hashtab;
static int mask;
static int *next_pos, *pnext_pos;

/* The log4 arrays were computed to mimick the behaviour of the log formula
   for computing the msp threshold in exon_cores(). For genomic_log4s,
   entry i stores the value for the length of a genomic sequence
   for which the contribution to the msp threshold is i/2, i.e.:
               1.4*log_4(3/4*len1) = i/2;  
   Similarly, cDNA_log4s entries store lengths of the cDNA sequence for which
   the contribution to the msp threshold is i/2, i.e.:
               1.4*log_4(len2) = i/2;
   Both arrays are sorted in increasing order, and can be searched with 
   binary search.
*/

GH/Sim4/sim4.2002-03-03/sim4b1.c  view on Meta::CPAN

    Exon     *tmp_block;


    if (in_K<=0) {
        /* compute expected length of longest exact match .. */
        /* K = (int) (log(.75*(double)len1)+log((double)len2))/log(4.0); */
        /* .. and throw in a fudge factor */
        /* K *= 1.4; */

        K = get_msp_threshold(len1, len2);
        if (K>=0) K--; /* compensate for the rounding in the log formula */
/*      commented this to avoid fragmentation 
        if (flag) K = min(K, DEFAULT_C); second pass 
*/
    } else 
        K = in_K;

    numMSPs = 0;
    exon_list = NULL;

    allocated = ckalloc((len1+len2+1)*sizeof(int));