diff --git a/src/overlapInCore/overlapInCore.C b/src/overlapInCore/overlapInCore.C index e80d953fb..43f4c9222 100644 --- a/src/overlapInCore/overlapInCore.C +++ b/src/overlapInCore/overlapInCore.C @@ -355,6 +355,20 @@ main(int argc, char **argv) { } else if (strcmp(argv[arg], "--hashload") == 0) { G.Max_Hash_Load = atof(argv[++arg]); +#if 0 + // This should still work, but not useful unless String_Ref_t is + // changed to uint32. + // + //fprintf(stderr, "--maxreadlen n For batches with all short reads, pack bits differently to\n"); + //fprintf(stderr, " process more reads per batch.\n"); + //fprintf(stderr, " all reads must be shorter than n\n"); + //fprintf(stderr, " limited to 2^(30-m) reads\n"); + //fprintf(stderr, " Common values:\n"); + //fprintf(stderr, " maxreadlen 2048->hashstrings 524288 (default)\n"); + //fprintf(stderr, " maxreadlen 512->hashstrings 2097152\n"); + //fprintf(stderr, " maxreadlen 128->hashstrings 8388608\n"); + //fprintf(stderr, "\n"); + } else if (strcmp(argv[arg], "--maxreadlen") == 0) { // Quite the gross way to do this, but simple. uint32 desired = strtoul(argv[++arg], NULL, 10); @@ -368,6 +382,7 @@ main(int argc, char **argv) { OFFSET_MASK = (1 << OFFSET_BITS) - 1; MAX_STRING_NUM = STRING_NUM_MASK; +#endif } else if (strcmp(argv[arg], "-o") == 0) { G.Outfile_Name = argv[++arg]; @@ -441,19 +456,9 @@ main(int argc, char **argv) { fprintf(stderr, "--minlength only output overlaps of or more bases\n"); fprintf(stderr, "\n"); fprintf(stderr, "--hashbits n Use n bits for the hash mask.\n"); - fprintf(stderr, "--hashstrings n Load at most n strings into the hash table at one time.\n"); fprintf(stderr, "--hashdatalen n Load at most n bytes into the hash table at one time.\n"); fprintf(stderr, "--hashload f Load to at most 0.0 < f < 1.0 capacity (default 0.7).\n"); fprintf(stderr, "\n"); - fprintf(stderr, "--maxreadlen n For batches with all short reads, pack bits differently to\n"); - fprintf(stderr, " process more reads per batch.\n"); - fprintf(stderr, " all reads must be shorter than n\n"); - fprintf(stderr, " --hashstrings limited to 2^(30-m)\n"); - fprintf(stderr, " Common values:\n"); - fprintf(stderr, " maxreadlen 2048->hashstrings 524288 (default)\n"); - fprintf(stderr, " maxreadlen 512->hashstrings 2097152\n"); - fprintf(stderr, " maxreadlen 128->hashstrings 8388608\n"); - fprintf(stderr, "\n"); fprintf(stderr, "--readsperbatch n Force batch size to n.\n"); fprintf(stderr, "--readsperthread n Force each thread to process n reads.\n"); fprintf(stderr, "\n");