| /dports/biology/gmap/gmap-2020-09-12/src/ |
| H A D | genome.c | 9848 low >>= (startdiscard+startdiscard);
9897 low >>= (startdiscard+startdiscard);
9915 high >>= (startdiscard+startdiscard);
10037 low >>= (startdiscard+startdiscard); in uncompress_mmap_nucleotides()
10068 low >>= (startdiscard+startdiscard); in uncompress_mmap_nucleotides()
10076 high >>= (startdiscard+startdiscard); in uncompress_mmap_nucleotides()
10173 low >>= (startdiscard+startdiscard); in uncompress_mmap_int_string()
10216 low >>= (startdiscard+startdiscard); in uncompress_mmap_int_string()
10229 high >>= (startdiscard+startdiscard); in uncompress_mmap_int_string()
10352 low >>= (startdiscard+startdiscard); in uncompress_mmap_int_string_convert()
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| H A D | genome_sites.c | 24717 int startdiscard, enddiscard; in Genome_print_blocks() local
24725 startdiscard = startpos % 32; in Genome_print_blocks()
24772 int startdiscard, enddiscard;
24780 startdiscard = startpos % 32;
24839 #define clear_start(diff,startdiscard) (diff & (~0U << (startdiscard))) argument
24842 #define clear_start_mask(startdiscard) (~0U << (startdiscard)) argument
24992 int startdiscard, enddiscard; in splicesite_positions() local
25330 int startdiscard, enddiscard; in splicesite_positions_novel() local
25520 int startdiscard, enddiscard; in prev_dinucleotide_position() local
25670 int startdiscard, enddiscard;
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| H A D | knownsplicing.c | 46 #define clear_start(diff,startdiscard) (diff & (~0U << (startdiscard))) argument
64 int startdiscard, enddiscard; in Knownsplicing_splicesite_p() local
71 startdiscard = (left+pos5) % 32; in Knownsplicing_splicesite_p()
77 splicesitep = clear_start(splicesitep,startdiscard); in Knownsplicing_splicesite_p()
85 if (32 - startdiscard >= enddiscard) { in Knownsplicing_splicesite_p()
91 splicesitep = clear_start(splicesitep,startdiscard); in Knownsplicing_splicesite_p()
115 splicesitep = clear_start(splicesitep,startdiscard); in Knownsplicing_splicesite_p()
133 if (enddiscard >= 32 - startdiscard) { in Knownsplicing_splicesite_p()
146 splicesitep = clear_start(splicesitep,startdiscard); in Knownsplicing_splicesite_p()
156 splicesitep = clear_start(splicesitep,startdiscard); in Knownsplicing_splicesite_p()
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| H A D | genome128_hr.c | 4191 #define clear_start_32(diff,startdiscard) (diff & (~0U << (startdiscard))) argument
4195 #define set_start_32(diff,startdiscard) (diff | ~(~0U << startdiscard)) argument
4199 #define clear_start_mask(startdiscard) (~0U << (startdiscard)) argument
4251 int startdiscard, enddiscard;
4445 int startdiscard, enddiscard;
4655 int startdiscard, enddiscard; in Genome_count_mismatches_substring_ref() local
4830 int startdiscard, enddiscard; in count_mismatches_substring_snps() local
5035 int startdiscard;
5166 int startdiscard, enddiscard; in mismatches_left() local
5429 int startdiscard, enddiscard; in mismatches_left_alt() local
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| H A D | genome128_consec.c | 3186 #define clear_start_32(diff,startdiscard) (diff & (~0U << (startdiscard))) argument
3190 #define set_start_32(diff,startdiscard) (diff | ~(~0U << startdiscard)) argument
3194 #define clear_start_mask(startdiscard) (~0U << (startdiscard)) argument
3246 int startdiscard, enddiscard; in Genome_consecutive_matches_rightward() local
3288 startdiscard = (left+pos5) % 32; in Genome_consecutive_matches_rightward()
3290 offset = -startdiscard + pos5; in Genome_consecutive_matches_rightward()
3512 int startdiscard, enddiscard; in Genome_consecutive_matches_leftward() local
3559 startdiscard = (left+pos5) % 32; in Genome_consecutive_matches_leftward()
3812 startdiscard = nshift2; in Genome_consecutive_matches_pair()
3829 offset = -startdiscard; in Genome_consecutive_matches_pair()
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| H A D | compress-write.c | 349 unsigned int startdiscard, enddiscard, i; in Compress_update_file() local
356 startdiscard = startpos % 32; in Compress_update_file()
374 for (i = startdiscard; i < enddiscard; i++) { in Compress_update_file()
395 for (i = startdiscard; i < 32; i++) { in Compress_update_file()
443 unsigned int startdiscard, enddiscard, i; in Compress_update_memory() local
448 startdiscard = startpos % 32; in Compress_update_memory()
468 for (i = startdiscard; i < enddiscard; i++) { in Compress_update_memory()
490 for (i = startdiscard; i < 32; i++) { in Compress_update_memory()
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| H A D | oligoindex_hr.c | 8908 int startdiscard, enddiscard;
21367 pos = startdiscard; in count_9mers_rev_partial()
21413 pos = startdiscard; in store_9mers_rev_partial()
21471 pos = startdiscard; in count_8mers_rev_partial()
21517 pos = startdiscard; in store_8mers_rev_partial()
21574 pos = startdiscard; in count_7mers_rev_partial()
21620 pos = startdiscard; in store_7mers_rev_partial()
21678 pos = startdiscard; in count_6mers_rev_partial()
21724 pos = startdiscard; in store_6mers_rev_partial()
21781 pos = startdiscard; in count_5mers_rev_partial()
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| H A D | splicetrie.c | 53 #define clear_start(diff,startdiscard) (diff & (~0U << (startdiscard))) argument
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| H A D | maxent_hr.c | 24723 int startdiscard, enddiscard; in Genome_print_blocks() local
24730 startdiscard = startpos % 32; in Genome_print_blocks()
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| /dports/biology/gmap/gmap-2020-09-12/ |
| H A D | ChangeLog | 8857 * oligoindex_hr.c: Fixed values for startdiscard and enddiscard in special
18351 * genome_hr.c: Fixed bug in mismatches_right_snps where startdiscard was not
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