181 static Genome_T genomebits_alt;  variable
1230 …Genome_count_mismatches_substring(&ref_nmismatches,genomebits,genomebits_alt,query_compress_fwd,le…  in single_hits_gplus()
1374 …Genome_count_mismatches_substring(&ref_nmismatches,genomebits,genomebits_alt,query_compress_rev,le…  in single_hits_gminus()
5314 							   /*ome*/genomebits,/*ome_alt*/genomebits_alt,query_compress_fwd,  in combine_ends_plus()
5429 								  /*ome*/genomebits,/*ome_alt*/genomebits_alt,query_compress_fwd,  in combine_ends_plus()
5504 …Genome_count_mismatches_substring(&ref_nmismatches2,genomebits,genomebits_alt,query_compress_fwd,l…  in combine_ends_plus()
5535 …Genome_count_mismatches_substring(&ref_nmismatches1,genomebits,genomebits_alt,query_compress_fwd,l…  in combine_ends_plus()
5588 …Genome_count_mismatches_substring(&ref_nmismatches2,genomebits,genomebits_alt,query_compress_fwd,l…  in combine_ends_plus()
5619 …Genome_count_mismatches_substring(&ref_nmismatches1,genomebits,genomebits_alt,query_compress_fwd,l…  in combine_ends_plus()
5674 …Genome_count_mismatches_substring(&ref_nmismatches2,genomebits,genomebits_alt,query_compress_fwd,l…  in combine_ends_plus()
5706 …Genome_count_mismatches_substring(&ref_nmismatches1,genomebits,genomebits_alt,query_compress_fwd,l…  in combine_ends_plus()
5843 							   /*ome*/genomebits,/*ome_alt*/genomebits_alt,query_compress_rev,  in combine_ends_minus()
5958 								  /*ome*/genomebits,/*ome_alt*/genomebits_alt,query_compress_rev,  in combine_ends_minus()
6035 …Genome_count_mismatches_substring(&ref_nmismatches1,genomebits,genomebits_alt,query_compress_rev,l…  in combine_ends_minus()
6067 …Genome_count_mismatches_substring(&ref_nmismatches2,genomebits,genomebits_alt,query_compress_rev,l…  in combine_ends_minus()
6120 …Genome_count_mismatches_substring(&ref_nmismatches1,genomebits,genomebits_alt,query_compress_rev,l…  in combine_ends_minus()
6152 …Genome_count_mismatches_substring(&ref_nmismatches2,genomebits,genomebits_alt,query_compress_rev,l…  in combine_ends_minus()
6208 …Genome_count_mismatches_substring(&ref_nmismatches1,genomebits,genomebits_alt,query_compress_rev,l…  in combine_ends_minus()
6242 …Genome_count_mismatches_substring(&ref_nmismatches2,genomebits,genomebits_alt,query_compress_rev,l…  in combine_ends_minus()
6872   genomebits_alt = genomebits_alt_in;  in Kmer_search_setup()