static char rcsid[] = "$Id: oligo.c 184203 2016-02-13 03:46:21Z twu $"; #ifdef HAVE_CONFIG_H #include #endif #include "oligo.h" #include #include #include "mem.h" #include "types.h" #include "indexdb_hr.h" #ifdef DEBUG #define debug(x) x #else #define debug(x) #endif /* Output of positions */ #ifdef DEBUG1 #define debug1(x) x #else #define debug1(x) #endif /* Oligo_repetitive_p */ #ifdef DEBUG2 #define debug2(x) x #else #define debug2(x) #endif #define NREPETITIVE 76 /* same for 6 through 15 */ static Oligospace_T repetitive_oligos_6[NREPETITIVE] = {0, /* AAAAAA */ 65, /* AACAAC */ 130, /* AAGAAG */ 195, /* AATAAT */ 260, /* ACAACA */ 273, /* ACACAC */ 325, /* ACCACC */ 390, /* ACGACG */ 455, /* ACTACT */ 520, /* AGAAGA */ 546, /* AGAGAG */ 585, /* AGCAGC */ 650, /* AGGAGG */ 715, /* AGTAGT */ 780, /* ATAATA */ 819, /* ATATAT */ 845, /* ATCATC */ 910, /* ATGATG */ 975, /* ATTATT */ 1040, /* CAACAA */ 1092, /* CACACA */ 1105, /* CACCAC */ 1170, /* CAGCAG */ 1235, /* CATCAT */ 1300, /* CCACCA */ 1365, /* CCCCCC */ 1430, /* CCGCCG */ 1495, /* CCTCCT */ 1560, /* CGACGA */ 1625, /* CGCCGC */ 1638, /* CGCGCG */ 1690, /* CGGCGG */ 1755, /* CGTCGT */ 1820, /* CTACTA */ 1885, /* CTCCTC */ 1911, /* CTCTCT */ 1950, /* CTGCTG */ 2015, /* CTTCTT */ 2080, /* GAAGAA */ 2145, /* GACGAC */ 2184, /* GAGAGA */ 2210, /* GAGGAG */ 2275, /* GATGAT */ 2340, /* GCAGCA */ 2405, /* GCCGCC */ 2457, /* GCGCGC */ 2470, /* GCGGCG */ 2535, /* GCTGCT */ 2600, /* GGAGGA */ 2665, /* GGCGGC */ 2730, /* GGGGGG */ 2795, /* GGTGGT */ 2860, /* GTAGTA */ 2925, /* GTCGTC */ 2990, /* GTGGTG */ 3003, /* GTGTGT */ 3055, /* GTTGTT */ 3120, /* TAATAA */ 3185, /* TACTAC */ 3250, /* TAGTAG */ 3276, /* TATATA */ 3315, /* TATTAT */ 3380, /* TCATCA */ 3445, /* TCCTCC */ 3510, /* TCGTCG */ 3549, /* TCTCTC */ 3575, /* TCTTCT */ 3640, /* TGATGA */ 3705, /* TGCTGC */ 3770, /* TGGTGG */ 3822, /* TGTGTG */ 3835, /* TGTTGT */ 3900, /* TTATTA */ 3965, /* TTCTTC */ 4030, /* TTGTTG */ 4095, /* TTTTTT */ }; static Oligospace_T repetitive_oligos_7[NREPETITIVE] = {0, /* AAAAAAA */ 260, /* AACAACA */ 520, /* AAGAAGA */ 780, /* AATAATA */ 1040, /* ACAACAA */ 1092, /* ACACACA */ 1300, /* ACCACCA */ 1560, /* ACGACGA */ 1820, /* ACTACTA */ 2080, /* AGAAGAA */ 2184, /* AGAGAGA */ 2340, /* AGCAGCA */ 2600, /* AGGAGGA */ 2860, /* AGTAGTA */ 3120, /* ATAATAA */ 3276, /* ATATATA */ 3380, /* ATCATCA */ 3640, /* ATGATGA */ 3900, /* ATTATTA */ 4161, /* CAACAAC */ 4369, /* CACACAC */ 4421, /* CACCACC */ 4681, /* CAGCAGC */ 4941, /* CATCATC */ 5201, /* CCACCAC */ 5461, /* CCCCCCC */ 5721, /* CCGCCGC */ 5981, /* CCTCCTC */ 6241, /* CGACGAC */ 6501, /* CGCCGCC */ 6553, /* CGCGCGC */ 6761, /* CGGCGGC */ 7021, /* CGTCGTC */ 7281, /* CTACTAC */ 7541, /* CTCCTCC */ 7645, /* CTCTCTC */ 7801, /* CTGCTGC */ 8061, /* CTTCTTC */ 8322, /* GAAGAAG */ 8582, /* GACGACG */ 8738, /* GAGAGAG */ 8842, /* GAGGAGG */ 9102, /* GATGATG */ 9362, /* GCAGCAG */ 9622, /* GCCGCCG */ 9830, /* GCGCGCG */ 9882, /* GCGGCGG */ 10142, /* GCTGCTG */ 10402, /* GGAGGAG */ 10662, /* GGCGGCG */ 10922, /* GGGGGGG */ 11182, /* GGTGGTG */ 11442, /* GTAGTAG */ 11702, /* GTCGTCG */ 11962, /* GTGGTGG */ 12014, /* GTGTGTG */ 12222, /* GTTGTTG */ 12483, /* TAATAAT */ 12743, /* TACTACT */ 13003, /* TAGTAGT */ 13107, /* TATATAT */ 13263, /* TATTATT */ 13523, /* TCATCAT */ 13783, /* TCCTCCT */ 14043, /* TCGTCGT */ 14199, /* TCTCTCT */ 14303, /* TCTTCTT */ 14563, /* TGATGAT */ 14823, /* TGCTGCT */ 15083, /* TGGTGGT */ 15291, /* TGTGTGT */ 15343, /* TGTTGTT */ 15603, /* TTATTAT */ 15863, /* TTCTTCT */ 16123, /* TTGTTGT */ 16383, /* TTTTTTT */ }; static Oligospace_T repetitive_oligos_8[NREPETITIVE] = {0, /* AAAAAAAA */ 1040, /* AACAACAA */ 2080, /* AAGAAGAA */ 3120, /* AATAATAA */ 4161, /* ACAACAAC */ 4369, /* ACACACAC */ 5201, /* ACCACCAC */ 6241, /* ACGACGAC */ 7281, /* ACTACTAC */ 8322, /* AGAAGAAG */ 8738, /* AGAGAGAG */ 9362, /* AGCAGCAG */ 10402, /* AGGAGGAG */ 11442, /* AGTAGTAG */ 12483, /* ATAATAAT */ 13107, /* ATATATAT */ 13523, /* ATCATCAT */ 14563, /* ATGATGAT */ 15603, /* ATTATTAT */ 16644, /* CAACAACA */ 17476, /* CACACACA */ 17684, /* CACCACCA */ 18724, /* CAGCAGCA */ 19764, /* CATCATCA */ 20805, /* CCACCACC */ 21845, /* CCCCCCCC */ 22885, /* CCGCCGCC */ 23925, /* CCTCCTCC */ 24966, /* CGACGACG */ 26006, /* CGCCGCCG */ 26214, /* CGCGCGCG */ 27046, /* CGGCGGCG */ 28086, /* CGTCGTCG */ 29127, /* CTACTACT */ 30167, /* CTCCTCCT */ 30583, /* CTCTCTCT */ 31207, /* CTGCTGCT */ 32247, /* CTTCTTCT */ 33288, /* GAAGAAGA */ 34328, /* GACGACGA */ 34952, /* GAGAGAGA */ 35368, /* GAGGAGGA */ 36408, /* GATGATGA */ 37449, /* GCAGCAGC */ 38489, /* GCCGCCGC */ 39321, /* GCGCGCGC */ 39529, /* GCGGCGGC */ 40569, /* GCTGCTGC */ 41610, /* GGAGGAGG */ 42650, /* GGCGGCGG */ 43690, /* GGGGGGGG */ 44730, /* GGTGGTGG */ 45771, /* GTAGTAGT */ 46811, /* GTCGTCGT */ 47851, /* GTGGTGGT */ 48059, /* GTGTGTGT */ 48891, /* GTTGTTGT */ 49932, /* TAATAATA */ 50972, /* TACTACTA */ 52012, /* TAGTAGTA */ 52428, /* TATATATA */ 53052, /* TATTATTA */ 54093, /* TCATCATC */ 55133, /* TCCTCCTC */ 56173, /* TCGTCGTC */ 56797, /* TCTCTCTC */ 57213, /* TCTTCTTC */ 58254, /* TGATGATG */ 59294, /* TGCTGCTG */ 60334, /* TGGTGGTG */ 61166, /* TGTGTGTG */ 61374, /* TGTTGTTG */ 62415, /* TTATTATT */ 63455, /* TTCTTCTT */ 64495, /* TTGTTGTT */ 65535, /* TTTTTTTT */ }; static Oligospace_T repetitive_oligos_9[NREPETITIVE] = {0, /* AAAAAAAAA */ 4161, /* AACAACAAC */ 8322, /* AAGAAGAAG */ 12483, /* AATAATAAT */ 16644, /* ACAACAACA */ 17476, /* ACACACACA */ 20805, /* ACCACCACC */ 24966, /* ACGACGACG */ 29127, /* ACTACTACT */ 33288, /* AGAAGAAGA */ 34952, /* AGAGAGAGA */ 37449, /* AGCAGCAGC */ 41610, /* AGGAGGAGG */ 45771, /* AGTAGTAGT */ 49932, /* ATAATAATA */ 52428, /* ATATATATA */ 54093, /* ATCATCATC */ 58254, /* ATGATGATG */ 62415, /* ATTATTATT */ 66576, /* CAACAACAA */ 69905, /* CACACACAC */ 70737, /* CACCACCAC */ 74898, /* CAGCAGCAG */ 79059, /* CATCATCAT */ 83220, /* CCACCACCA */ 87381, /* CCCCCCCCC */ 91542, /* CCGCCGCCG */ 95703, /* CCTCCTCCT */ 99864, /* CGACGACGA */ 104025, /* CGCCGCCGC */ 104857, /* CGCGCGCGC */ 108186, /* CGGCGGCGG */ 112347, /* CGTCGTCGT */ 116508, /* CTACTACTA */ 120669, /* CTCCTCCTC */ 122333, /* CTCTCTCTC */ 124830, /* CTGCTGCTG */ 128991, /* CTTCTTCTT */ 133152, /* GAAGAAGAA */ 137313, /* GACGACGAC */ 139810, /* GAGAGAGAG */ 141474, /* GAGGAGGAG */ 145635, /* GATGATGAT */ 149796, /* GCAGCAGCA */ 153957, /* GCCGCCGCC */ 157286, /* GCGCGCGCG */ 158118, /* GCGGCGGCG */ 162279, /* GCTGCTGCT */ 166440, /* GGAGGAGGA */ 170601, /* GGCGGCGGC */ 174762, /* GGGGGGGGG */ 178923, /* GGTGGTGGT */ 183084, /* GTAGTAGTA */ 187245, /* GTCGTCGTC */ 191406, /* GTGGTGGTG */ 192238, /* GTGTGTGTG */ 195567, /* GTTGTTGTT */ 199728, /* TAATAATAA */ 203889, /* TACTACTAC */ 208050, /* TAGTAGTAG */ 209715, /* TATATATAT */ 212211, /* TATTATTAT */ 216372, /* TCATCATCA */ 220533, /* TCCTCCTCC */ 224694, /* TCGTCGTCG */ 227191, /* TCTCTCTCT */ 228855, /* TCTTCTTCT */ 233016, /* TGATGATGA */ 237177, /* TGCTGCTGC */ 241338, /* TGGTGGTGG */ 244667, /* TGTGTGTGT */ 245499, /* TGTTGTTGT */ 249660, /* TTATTATTA */ 253821, /* TTCTTCTTC */ 257982, /* TTGTTGTTG */ 262143, /* TTTTTTTTT */ }; static Oligospace_T repetitive_oligos_10[NREPETITIVE] = {0, /* AAAAAAAAAA */ 16644, /* AACAACAACA */ 33288, /* AAGAAGAAGA */ 49932, /* AATAATAATA */ 66576, /* ACAACAACAA */ 69905, /* ACACACACAC */ 83220, /* ACCACCACCA */ 99864, /* ACGACGACGA */ 116508, /* ACTACTACTA */ 133152, /* AGAAGAAGAA */ 139810, /* AGAGAGAGAG */ 149796, /* AGCAGCAGCA */ 166440, /* AGGAGGAGGA */ 183084, /* AGTAGTAGTA */ 199728, /* ATAATAATAA */ 209715, /* ATATATATAT */ 216372, /* ATCATCATCA */ 233016, /* ATGATGATGA */ 249660, /* ATTATTATTA */ 266305, /* CAACAACAAC */ 279620, /* CACACACACA */ 282949, /* CACCACCACC */ 299593, /* CAGCAGCAGC */ 316237, /* CATCATCATC */ 332881, /* CCACCACCAC */ 349525, /* CCCCCCCCCC */ 366169, /* CCGCCGCCGC */ 382813, /* CCTCCTCCTC */ 399457, /* CGACGACGAC */ 416101, /* CGCCGCCGCC */ 419430, /* CGCGCGCGCG */ 432745, /* CGGCGGCGGC */ 449389, /* CGTCGTCGTC */ 466033, /* CTACTACTAC */ 482677, /* CTCCTCCTCC */ 489335, /* CTCTCTCTCT */ 499321, /* CTGCTGCTGC */ 515965, /* CTTCTTCTTC */ 532610, /* GAAGAAGAAG */ 549254, /* GACGACGACG */ 559240, /* GAGAGAGAGA */ 565898, /* GAGGAGGAGG */ 582542, /* GATGATGATG */ 599186, /* GCAGCAGCAG */ 615830, /* GCCGCCGCCG */ 629145, /* GCGCGCGCGC */ 632474, /* GCGGCGGCGG */ 649118, /* GCTGCTGCTG */ 665762, /* GGAGGAGGAG */ 682406, /* GGCGGCGGCG */ 699050, /* GGGGGGGGGG */ 715694, /* GGTGGTGGTG */ 732338, /* GTAGTAGTAG */ 748982, /* GTCGTCGTCG */ 765626, /* GTGGTGGTGG */ 768955, /* GTGTGTGTGT */ 782270, /* GTTGTTGTTG */ 798915, /* TAATAATAAT */ 815559, /* TACTACTACT */ 832203, /* TAGTAGTAGT */ 838860, /* TATATATATA */ 848847, /* TATTATTATT */ 865491, /* TCATCATCAT */ 882135, /* TCCTCCTCCT */ 898779, /* TCGTCGTCGT */ 908765, /* TCTCTCTCTC */ 915423, /* TCTTCTTCTT */ 932067, /* TGATGATGAT */ 948711, /* TGCTGCTGCT */ 965355, /* TGGTGGTGGT */ 978670, /* TGTGTGTGTG */ 981999, /* TGTTGTTGTT */ 998643, /* TTATTATTAT */ 1015287, /* TTCTTCTTCT */ 1031931, /* TTGTTGTTGT */ 1048575, /* TTTTTTTTTT */ }; static Oligospace_T repetitive_oligos_11[NREPETITIVE] = {0, /* AAAAAAAAAAA */ 66576, /* AACAACAACAA */ 133152, /* AAGAAGAAGAA */ 199728, /* AATAATAATAA */ 266305, /* ACAACAACAAC */ 279620, /* ACACACACACA */ 332881, /* ACCACCACCAC */ 399457, /* ACGACGACGAC */ 466033, /* ACTACTACTAC */ 532610, /* AGAAGAAGAAG */ 559240, /* AGAGAGAGAGA */ 599186, /* AGCAGCAGCAG */ 665762, /* AGGAGGAGGAG */ 732338, /* AGTAGTAGTAG */ 798915, /* ATAATAATAAT */ 838860, /* ATATATATATA */ 865491, /* ATCATCATCAT */ 932067, /* ATGATGATGAT */ 998643, /* ATTATTATTAT */ 1065220, /* CAACAACAACA */ 1118481, /* CACACACACAC */ 1131796, /* CACCACCACCA */ 1198372, /* CAGCAGCAGCA */ 1264948, /* CATCATCATCA */ 1331525, /* CCACCACCACC */ 1398101, /* CCCCCCCCCCC */ 1464677, /* CCGCCGCCGCC */ 1531253, /* CCTCCTCCTCC */ 1597830, /* CGACGACGACG */ 1664406, /* CGCCGCCGCCG */ 1677721, /* CGCGCGCGCGC */ 1730982, /* CGGCGGCGGCG */ 1797558, /* CGTCGTCGTCG */ 1864135, /* CTACTACTACT */ 1930711, /* CTCCTCCTCCT */ 1957341, /* CTCTCTCTCTC */ 1997287, /* CTGCTGCTGCT */ 2063863, /* CTTCTTCTTCT */ 2130440, /* GAAGAAGAAGA */ 2197016, /* GACGACGACGA */ 2236962, /* GAGAGAGAGAG */ 2263592, /* GAGGAGGAGGA */ 2330168, /* GATGATGATGA */ 2396745, /* GCAGCAGCAGC */ 2463321, /* GCCGCCGCCGC */ 2516582, /* GCGCGCGCGCG */ 2529897, /* GCGGCGGCGGC */ 2596473, /* GCTGCTGCTGC */ 2663050, /* GGAGGAGGAGG */ 2729626, /* GGCGGCGGCGG */ 2796202, /* GGGGGGGGGGG */ 2862778, /* GGTGGTGGTGG */ 2929355, /* GTAGTAGTAGT */ 2995931, /* GTCGTCGTCGT */ 3062507, /* GTGGTGGTGGT */ 3075822, /* GTGTGTGTGTG */ 3129083, /* GTTGTTGTTGT */ 3195660, /* TAATAATAATA */ 3262236, /* TACTACTACTA */ 3328812, /* TAGTAGTAGTA */ 3355443, /* TATATATATAT */ 3395388, /* TATTATTATTA */ 3461965, /* TCATCATCATC */ 3528541, /* TCCTCCTCCTC */ 3595117, /* TCGTCGTCGTC */ 3635063, /* TCTCTCTCTCT */ 3661693, /* TCTTCTTCTTC */ 3728270, /* TGATGATGATG */ 3794846, /* TGCTGCTGCTG */ 3861422, /* TGGTGGTGGTG */ 3914683, /* TGTGTGTGTGT */ 3927998, /* TGTTGTTGTTG */ 3994575, /* TTATTATTATT */ 4061151, /* TTCTTCTTCTT */ 4127727, /* TTGTTGTTGTT */ 4194303, /* TTTTTTTTTTT */ }; static Oligospace_T repetitive_oligos_12[NREPETITIVE] = {0, /* AAAAAAAAAAAA */ 266305, /* AACAACAACAAC */ 532610, /* AAGAAGAAGAAG */ 798915, /* AATAATAATAAT */ 1065220, /* ACAACAACAACA */ 1118481, /* ACACACACACAC */ 1331525, /* ACCACCACCACC */ 1597830, /* ACGACGACGACG */ 1864135, /* ACTACTACTACT */ 2130440, /* AGAAGAAGAAGA */ 2236962, /* AGAGAGAGAGAG */ 2396745, /* AGCAGCAGCAGC */ 2663050, /* AGGAGGAGGAGG */ 2929355, /* AGTAGTAGTAGT */ 3195660, /* ATAATAATAATA */ 3355443, /* ATATATATATAT */ 3461965, /* ATCATCATCATC */ 3728270, /* ATGATGATGATG */ 3994575, /* ATTATTATTATT */ 4260880, /* CAACAACAACAA */ 4473924, /* CACACACACACA */ 4527185, /* CACCACCACCAC */ 4793490, /* CAGCAGCAGCAG */ 5059795, /* CATCATCATCAT */ 5326100, /* CCACCACCACCA */ 5592405, /* CCCCCCCCCCCC */ 5858710, /* CCGCCGCCGCCG */ 6125015, /* CCTCCTCCTCCT */ 6391320, /* CGACGACGACGA */ 6657625, /* CGCCGCCGCCGC */ 6710886, /* CGCGCGCGCGCG */ 6923930, /* CGGCGGCGGCGG */ 7190235, /* CGTCGTCGTCGT */ 7456540, /* CTACTACTACTA */ 7722845, /* CTCCTCCTCCTC */ 7829367, /* CTCTCTCTCTCT */ 7989150, /* CTGCTGCTGCTG */ 8255455, /* CTTCTTCTTCTT */ 8521760, /* GAAGAAGAAGAA */ 8788065, /* GACGACGACGAC */ 8947848, /* GAGAGAGAGAGA */ 9054370, /* GAGGAGGAGGAG */ 9320675, /* GATGATGATGAT */ 9586980, /* GCAGCAGCAGCA */ 9853285, /* GCCGCCGCCGCC */ 10066329, /* GCGCGCGCGCGC */ 10119590, /* GCGGCGGCGGCG */ 10385895, /* GCTGCTGCTGCT */ 10652200, /* GGAGGAGGAGGA */ 10918505, /* GGCGGCGGCGGC */ 11184810, /* GGGGGGGGGGGG */ 11451115, /* GGTGGTGGTGGT */ 11717420, /* GTAGTAGTAGTA */ 11983725, /* GTCGTCGTCGTC */ 12250030, /* GTGGTGGTGGTG */ 12303291, /* GTGTGTGTGTGT */ 12516335, /* GTTGTTGTTGTT */ 12782640, /* TAATAATAATAA */ 13048945, /* TACTACTACTAC */ 13315250, /* TAGTAGTAGTAG */ 13421772, /* TATATATATATA */ 13581555, /* TATTATTATTAT */ 13847860, /* TCATCATCATCA */ 14114165, /* TCCTCCTCCTCC */ 14380470, /* TCGTCGTCGTCG */ 14540253, /* TCTCTCTCTCTC */ 14646775, /* TCTTCTTCTTCT */ 14913080, /* TGATGATGATGA */ 15179385, /* TGCTGCTGCTGC */ 15445690, /* TGGTGGTGGTGG */ 15658734, /* TGTGTGTGTGTG */ 15711995, /* TGTTGTTGTTGT */ 15978300, /* TTATTATTATTA */ 16244605, /* TTCTTCTTCTTC */ 16510910, /* TTGTTGTTGTTG */ 16777215, /* TTTTTTTTTTTT */ }; static Oligospace_T repetitive_oligos_13[NREPETITIVE] = {0, /* AAAAAAAAAAAAA */ 1065220, /* AACAACAACAACA */ 2130440, /* AAGAAGAAGAAGA */ 3195660, /* AATAATAATAATA */ 4260880, /* ACAACAACAACAA */ 4473924, /* ACACACACACACA */ 5326100, /* ACCACCACCACCA */ 6391320, /* ACGACGACGACGA */ 7456540, /* ACTACTACTACTA */ 8521760, /* AGAAGAAGAAGAA */ 8947848, /* AGAGAGAGAGAGA */ 9586980, /* AGCAGCAGCAGCA */ 10652200, /* AGGAGGAGGAGGA */ 11717420, /* AGTAGTAGTAGTA */ 12782640, /* ATAATAATAATAA */ 13421772, /* ATATATATATATA */ 13847860, /* ATCATCATCATCA */ 14913080, /* ATGATGATGATGA */ 15978300, /* ATTATTATTATTA */ 17043521, /* CAACAACAACAAC */ 17895697, /* CACACACACACAC */ 18108741, /* CACCACCACCACC */ 19173961, /* CAGCAGCAGCAGC */ 20239181, /* CATCATCATCATC */ 21304401, /* CCACCACCACCAC */ 22369621, /* CCCCCCCCCCCCC */ 23434841, /* CCGCCGCCGCCGC */ 24500061, /* CCTCCTCCTCCTC */ 25565281, /* CGACGACGACGAC */ 26630501, /* CGCCGCCGCCGCC */ 26843545, /* CGCGCGCGCGCGC */ 27695721, /* CGGCGGCGGCGGC */ 28760941, /* CGTCGTCGTCGTC */ 29826161, /* CTACTACTACTAC */ 30891381, /* CTCCTCCTCCTCC */ 31317469, /* CTCTCTCTCTCTC */ 31956601, /* CTGCTGCTGCTGC */ 33021821, /* CTTCTTCTTCTTC */ 34087042, /* GAAGAAGAAGAAG */ 35152262, /* GACGACGACGACG */ 35791394, /* GAGAGAGAGAGAG */ 36217482, /* GAGGAGGAGGAGG */ 37282702, /* GATGATGATGATG */ 38347922, /* GCAGCAGCAGCAG */ 39413142, /* GCCGCCGCCGCCG */ 40265318, /* GCGCGCGCGCGCG */ 40478362, /* GCGGCGGCGGCGG */ 41543582, /* GCTGCTGCTGCTG */ 42608802, /* GGAGGAGGAGGAG */ 43674022, /* GGCGGCGGCGGCG */ 44739242, /* GGGGGGGGGGGGG */ 45804462, /* GGTGGTGGTGGTG */ 46869682, /* GTAGTAGTAGTAG */ 47934902, /* GTCGTCGTCGTCG */ 49000122, /* GTGGTGGTGGTGG */ 49213166, /* GTGTGTGTGTGTG */ 50065342, /* GTTGTTGTTGTTG */ 51130563, /* TAATAATAATAAT */ 52195783, /* TACTACTACTACT */ 53261003, /* TAGTAGTAGTAGT */ 53687091, /* TATATATATATAT */ 54326223, /* TATTATTATTATT */ 55391443, /* TCATCATCATCAT */ 56456663, /* TCCTCCTCCTCCT */ 57521883, /* TCGTCGTCGTCGT */ 58161015, /* TCTCTCTCTCTCT */ 58587103, /* TCTTCTTCTTCTT */ 59652323, /* TGATGATGATGAT */ 60717543, /* TGCTGCTGCTGCT */ 61782763, /* TGGTGGTGGTGGT */ 62634939, /* TGTGTGTGTGTGT */ 62847983, /* TGTTGTTGTTGTT */ 63913203, /* TTATTATTATTAT */ 64978423, /* TTCTTCTTCTTCT */ 66043643, /* TTGTTGTTGTTGT */ 67108863, /* TTTTTTTTTTTTT */ }; static Oligospace_T repetitive_oligos_14[NREPETITIVE] = {0, /* AAAAAAAAAAAAAA */ 4260880, /* AACAACAACAACAA */ 8521760, /* AAGAAGAAGAAGAA */ 12782640, /* AATAATAATAATAA */ 17043521, /* ACAACAACAACAAC */ 17895697, /* ACACACACACACAC */ 21304401, /* ACCACCACCACCAC */ 25565281, /* ACGACGACGACGAC */ 29826161, /* ACTACTACTACTAC */ 34087042, /* AGAAGAAGAAGAAG */ 35791394, /* AGAGAGAGAGAGAG */ 38347922, /* AGCAGCAGCAGCAG */ 42608802, /* AGGAGGAGGAGGAG */ 46869682, /* AGTAGTAGTAGTAG */ 51130563, /* ATAATAATAATAAT */ 53687091, /* ATATATATATATAT */ 55391443, /* ATCATCATCATCAT */ 59652323, /* ATGATGATGATGAT */ 63913203, /* ATTATTATTATTAT */ 68174084, /* CAACAACAACAACA */ 71582788, /* CACACACACACACA */ 72434964, /* CACCACCACCACCA */ 76695844, /* CAGCAGCAGCAGCA */ 80956724, /* CATCATCATCATCA */ 85217605, /* CCACCACCACCACC */ 89478485, /* CCCCCCCCCCCCCC */ 93739365, /* CCGCCGCCGCCGCC */ 98000245, /* CCTCCTCCTCCTCC */ 102261126, /* CGACGACGACGACG */ 106522006, /* CGCCGCCGCCGCCG */ 107374182, /* CGCGCGCGCGCGCG */ 110782886, /* CGGCGGCGGCGGCG */ 115043766, /* CGTCGTCGTCGTCG */ 119304647, /* CTACTACTACTACT */ 123565527, /* CTCCTCCTCCTCCT */ 125269879, /* CTCTCTCTCTCTCT */ 127826407, /* CTGCTGCTGCTGCT */ 132087287, /* CTTCTTCTTCTTCT */ 136348168, /* GAAGAAGAAGAAGA */ 140609048, /* GACGACGACGACGA */ 143165576, /* GAGAGAGAGAGAGA */ 144869928, /* GAGGAGGAGGAGGA */ 149130808, /* GATGATGATGATGA */ 153391689, /* GCAGCAGCAGCAGC */ 157652569, /* GCCGCCGCCGCCGC */ 161061273, /* GCGCGCGCGCGCGC */ 161913449, /* GCGGCGGCGGCGGC */ 166174329, /* GCTGCTGCTGCTGC */ 170435210, /* GGAGGAGGAGGAGG */ 174696090, /* GGCGGCGGCGGCGG */ 178956970, /* GGGGGGGGGGGGGG */ 183217850, /* GGTGGTGGTGGTGG */ 187478731, /* GTAGTAGTAGTAGT */ 191739611, /* GTCGTCGTCGTCGT */ 196000491, /* GTGGTGGTGGTGGT */ 196852667, /* GTGTGTGTGTGTGT */ 200261371, /* GTTGTTGTTGTTGT */ 204522252, /* TAATAATAATAATA */ 208783132, /* TACTACTACTACTA */ 213044012, /* TAGTAGTAGTAGTA */ 214748364, /* TATATATATATATA */ 217304892, /* TATTATTATTATTA */ 221565773, /* TCATCATCATCATC */ 225826653, /* TCCTCCTCCTCCTC */ 230087533, /* TCGTCGTCGTCGTC */ 232644061, /* TCTCTCTCTCTCTC */ 234348413, /* TCTTCTTCTTCTTC */ 238609294, /* TGATGATGATGATG */ 242870174, /* TGCTGCTGCTGCTG */ 247131054, /* TGGTGGTGGTGGTG */ 250539758, /* TGTGTGTGTGTGTG */ 251391934, /* TGTTGTTGTTGTTG */ 255652815, /* TTATTATTATTATT */ 259913695, /* TTCTTCTTCTTCTT */ 264174575, /* TTGTTGTTGTTGTT */ 268435455, /* TTTTTTTTTTTTTT */ }; static Oligospace_T repetitive_oligos_15[NREPETITIVE] = {0, /* AAAAAAAAAAAAAAA */ 17043521, /* AACAACAACAACAAC */ 34087042, /* AAGAAGAAGAAGAAG */ 51130563, /* AATAATAATAATAAT */ 68174084, /* ACAACAACAACAACA */ 71582788, /* ACACACACACACACA */ 85217605, /* ACCACCACCACCACC */ 102261126, /* ACGACGACGACGACG */ 119304647, /* ACTACTACTACTACT */ 136348168, /* AGAAGAAGAAGAAGA */ 143165576, /* AGAGAGAGAGAGAGA */ 153391689, /* AGCAGCAGCAGCAGC */ 170435210, /* AGGAGGAGGAGGAGG */ 187478731, /* AGTAGTAGTAGTAGT */ 204522252, /* ATAATAATAATAATA */ 214748364, /* ATATATATATATATA */ 221565773, /* ATCATCATCATCATC */ 238609294, /* ATGATGATGATGATG */ 255652815, /* ATTATTATTATTATT */ 272696336, /* CAACAACAACAACAA */ 286331153, /* CACACACACACACAC */ 289739857, /* CACCACCACCACCAC */ 306783378, /* CAGCAGCAGCAGCAG */ 323826899, /* CATCATCATCATCAT */ 340870420, /* CCACCACCACCACCA */ 357913941, /* CCCCCCCCCCCCCCC */ 374957462, /* CCGCCGCCGCCGCCG */ 392000983, /* CCTCCTCCTCCTCCT */ 409044504, /* CGACGACGACGACGA */ 426088025, /* CGCCGCCGCCGCCGC */ 429496729, /* CGCGCGCGCGCGCGC */ 443131546, /* CGGCGGCGGCGGCGG */ 460175067, /* CGTCGTCGTCGTCGT */ 477218588, /* CTACTACTACTACTA */ 494262109, /* CTCCTCCTCCTCCTC */ 501079517, /* CTCTCTCTCTCTCTC */ 511305630, /* CTGCTGCTGCTGCTG */ 528349151, /* CTTCTTCTTCTTCTT */ 545392672, /* GAAGAAGAAGAAGAA */ 562436193, /* GACGACGACGACGAC */ 572662306, /* GAGAGAGAGAGAGAG */ 579479714, /* GAGGAGGAGGAGGAG */ 596523235, /* GATGATGATGATGAT */ 613566756, /* GCAGCAGCAGCAGCA */ 630610277, /* GCCGCCGCCGCCGCC */ 644245094, /* GCGCGCGCGCGCGCG */ 647653798, /* GCGGCGGCGGCGGCG */ 664697319, /* GCTGCTGCTGCTGCT */ 681740840, /* GGAGGAGGAGGAGGA */ 698784361, /* GGCGGCGGCGGCGGC */ 715827882, /* GGGGGGGGGGGGGGG */ 732871403, /* GGTGGTGGTGGTGGT */ 749914924, /* GTAGTAGTAGTAGTA */ 766958445, /* GTCGTCGTCGTCGTC */ 784001966, /* GTGGTGGTGGTGGTG */ 787410670, /* GTGTGTGTGTGTGTG */ 801045487, /* GTTGTTGTTGTTGTT */ 818089008, /* TAATAATAATAATAA */ 835132529, /* TACTACTACTACTAC */ 852176050, /* TAGTAGTAGTAGTAG */ 858993459, /* TATATATATATATAT */ 869219571, /* TATTATTATTATTAT */ 886263092, /* TCATCATCATCATCA */ 903306613, /* TCCTCCTCCTCCTCC */ 920350134, /* TCGTCGTCGTCGTCG */ 930576247, /* TCTCTCTCTCTCTCT */ 937393655, /* TCTTCTTCTTCTTCT */ 954437176, /* TGATGATGATGATGA */ 971480697, /* TGCTGCTGCTGCTGC */ 988524218, /* TGGTGGTGGTGGTGG */ 1002159035, /* TGTGTGTGTGTGTGT */ 1005567739, /* TGTTGTTGTTGTTGT */ 1022611260, /* TTATTATTATTATTA */ 1039654781, /* TTCTTCTTCTTCTTC */ 1056698302, /* TTGTTGTTGTTGTTG */ 1073741823, /* TTTTTTTTTTTTTTT */ }; static Oligospace_T repetitive_oligos_16[NREPETITIVE] = {0, /* AAAAAAAAAAAAAAAA */ 68174084, /* AACAACAACAACAACA */ 136348168, /* AAGAAGAAGAAGAAGA */ 204522252, /* AATAATAATAATAATA */ 272696336, /* ACAACAACAACAACAA */ 286331153, /* ACACACACACACACAC */ 340870420, /* ACCACCACCACCACCA */ 409044504, /* ACGACGACGACGACGA */ 477218588, /* ACTACTACTACTACTA */ 545392672, /* AGAAGAAGAAGAAGAA */ 572662306, /* AGAGAGAGAGAGAGAG */ 613566756, /* AGCAGCAGCAGCAGCA */ 681740840, /* AGGAGGAGGAGGAGGA */ 749914924, /* AGTAGTAGTAGTAGTA */ 818089008, /* ATAATAATAATAATAA */ 858993459, /* ATATATATATATATAT */ 886263092, /* ATCATCATCATCATCA */ 954437176, /* ATGATGATGATGATGA */ 1022611260, /* ATTATTATTATTATTA */ 1090785345, /* CAACAACAACAACAAC */ 1145324612, /* CACACACACACACACA */ 1158959429, /* CACCACCACCACCACC */ 1227133513, /* CAGCAGCAGCAGCAGC */ 1295307597, /* CATCATCATCATCATC */ 1363481681, /* CCACCACCACCACCAC */ 1431655765, /* CCCCCCCCCCCCCCCC */ 1499829849, /* CCGCCGCCGCCGCCGC */ 1568003933, /* CCTCCTCCTCCTCCTC */ 1636178017, /* CGACGACGACGACGAC */ 1704352101, /* CGCCGCCGCCGCCGCC */ 1717986918, /* CGCGCGCGCGCGCGCG */ 1772526185, /* CGGCGGCGGCGGCGGC */ 1840700269, /* CGTCGTCGTCGTCGTC */ 1908874353, /* CTACTACTACTACTAC */ 1977048437, /* CTCCTCCTCCTCCTCC */ 2004318071, /* CTCTCTCTCTCTCTCT */ 2045222521, /* CTGCTGCTGCTGCTGC */ 2113396605, /* CTTCTTCTTCTTCTTC */ 2181570690, /* GAAGAAGAAGAAGAAG */ 2249744774, /* GACGACGACGACGACG */ 2290649224, /* GAGAGAGAGAGAGAGA */ 2317918858, /* GAGGAGGAGGAGGAGG */ 2386092942, /* GATGATGATGATGATG */ 2454267026, /* GCAGCAGCAGCAGCAG */ 2522441110, /* GCCGCCGCCGCCGCCG */ 2576980377, /* GCGCGCGCGCGCGCGC */ 2590615194, /* GCGGCGGCGGCGGCGG */ 2658789278, /* GCTGCTGCTGCTGCTG */ 2726963362, /* GGAGGAGGAGGAGGAG */ 2795137446, /* GGCGGCGGCGGCGGCG */ 2863311530, /* GGGGGGGGGGGGGGGG */ 2931485614, /* GGTGGTGGTGGTGGTG */ 2999659698, /* GTAGTAGTAGTAGTAG */ 3067833782, /* GTCGTCGTCGTCGTCG */ 3136007866, /* GTGGTGGTGGTGGTGG */ 3149642683, /* GTGTGTGTGTGTGTGT */ 3204181950, /* GTTGTTGTTGTTGTTG */ 3272356035, /* TAATAATAATAATAAT */ 3340530119, /* TACTACTACTACTACT */ 3408704203, /* TAGTAGTAGTAGTAGT */ 3435973836, /* TATATATATATATATA */ 3476878287, /* TATTATTATTATTATT */ 3545052371, /* TCATCATCATCATCAT */ 3613226455, /* TCCTCCTCCTCCTCCT */ 3681400539, /* TCGTCGTCGTCGTCGT */ 3722304989, /* TCTCTCTCTCTCTCTC */ 3749574623, /* TCTTCTTCTTCTTCTT */ 3817748707, /* TGATGATGATGATGAT */ 3885922791, /* TGCTGCTGCTGCTGCT */ 3954096875, /* TGGTGGTGGTGGTGGT */ 4008636142, /* TGTGTGTGTGTGTGTG */ 4022270959, /* TGTTGTTGTTGTTGTT */ 4090445043, /* TTATTATTATTATTAT */ 4158619127, /* TTCTTCTTCTTCTTCT */ 4226793211, /* TTGTTGTTGTTGTTGT */ 4294967295, /* TTTTTTTTTTTTTTTT */ }; static Oligospace_T repetitive_oligos_17[NREPETITIVE] = {0, /* AAAAAAAAAAAAAAAAA */ 272696336, /* AACAACAACAACAACAA */ 545392672, /* AAGAAGAAGAAGAAGAA */ 818089008, /* AATAATAATAATAATAA */ 1090785345, /* ACAACAACAACAACAAC */ 1145324612, /* ACACACACACACACACA */ 1363481681, /* ACCACCACCACCACCAC */ 1636178017, /* ACGACGACGACGACGAC */ 1908874353, /* ACTACTACTACTACTAC */ 2181570690, /* AGAAGAAGAAGAAGAAG */ 2290649224, /* AGAGAGAGAGAGAGAGA */ 2454267026, /* AGCAGCAGCAGCAGCAG */ 2726963362, /* AGGAGGAGGAGGAGGAG */ 2999659698, /* AGTAGTAGTAGTAGTAG */ 3272356035, /* ATAATAATAATAATAAT */ 3435973836, /* ATATATATATATATATA */ 3545052371, /* ATCATCATCATCATCAT */ 3817748707, /* ATGATGATGATGATGAT */ 4090445043, /* ATTATTATTATTATTAT */ 4363141380, /* CAACAACAACAACAACA */ 4581298449, /* CACACACACACACACAC */ 4635837716, /* CACCACCACCACCACCA */ 4908534052, /* CAGCAGCAGCAGCAGCA */ 5181230388, /* CATCATCATCATCATCA */ 5453926725, /* CCACCACCACCACCACC */ 5726623061, /* CCCCCCCCCCCCCCCCC */ 5999319397, /* CCGCCGCCGCCGCCGCC */ 6272015733, /* CCTCCTCCTCCTCCTCC */ 6544712070, /* CGACGACGACGACGACG */ 6817408406, /* CGCCGCCGCCGCCGCCG */ 6871947673, /* CGCGCGCGCGCGCGCGC */ 7090104742, /* CGGCGGCGGCGGCGGCG */ 7362801078, /* CGTCGTCGTCGTCGTCG */ 7635497415, /* CTACTACTACTACTACT */ 7908193751, /* CTCCTCCTCCTCCTCCT */ 8017272285, /* CTCTCTCTCTCTCTCTC */ 8180890087, /* CTGCTGCTGCTGCTGCT */ 8453586423, /* CTTCTTCTTCTTCTTCT */ 8726282760, /* GAAGAAGAAGAAGAAGA */ 8998979096, /* GACGACGACGACGACGA */ 9162596898, /* GAGAGAGAGAGAGAGAG */ 9271675432, /* GAGGAGGAGGAGGAGGA */ 9544371768, /* GATGATGATGATGATGA */ 9817068105, /* GCAGCAGCAGCAGCAGC */ 10089764441, /* GCCGCCGCCGCCGCCGC */ 10307921510, /* GCGCGCGCGCGCGCGCG */ 10362460777, /* GCGGCGGCGGCGGCGGC */ 10635157113, /* GCTGCTGCTGCTGCTGC */ 10907853450, /* GGAGGAGGAGGAGGAGG */ 11180549786, /* GGCGGCGGCGGCGGCGG */ 11453246122, /* GGGGGGGGGGGGGGGGG */ 11725942458, /* GGTGGTGGTGGTGGTGG */ 11998638795, /* GTAGTAGTAGTAGTAGT */ 12271335131, /* GTCGTCGTCGTCGTCGT */ 12544031467, /* GTGGTGGTGGTGGTGGT */ 12598570734, /* GTGTGTGTGTGTGTGTG */ 12816727803, /* GTTGTTGTTGTTGTTGT */ 13089424140, /* TAATAATAATAATAATA */ 13362120476, /* TACTACTACTACTACTA */ 13634816812, /* TAGTAGTAGTAGTAGTA */ 13743895347, /* TATATATATATATATAT */ 13907513148, /* TATTATTATTATTATTA */ 14180209485, /* TCATCATCATCATCATC */ 14452905821, /* TCCTCCTCCTCCTCCTC */ 14725602157, /* TCGTCGTCGTCGTCGTC */ 14889219959, /* TCTCTCTCTCTCTCTCT */ 14998298493, /* TCTTCTTCTTCTTCTTC */ 15270994830, /* TGATGATGATGATGATG */ 15543691166, /* TGCTGCTGCTGCTGCTG */ 15816387502, /* TGGTGGTGGTGGTGGTG */ 16034544571, /* TGTGTGTGTGTGTGTGT */ 16089083838, /* TGTTGTTGTTGTTGTTG */ 16361780175, /* TTATTATTATTATTATT */ 16634476511, /* TTCTTCTTCTTCTTCTT */ 16907172847, /* TTGTTGTTGTTGTTGTT */ 17179869183, /* TTTTTTTTTTTTTTTTT */ }; static Oligospace_T repetitive_oligos_18[NREPETITIVE] = {0, /* AAAAAAAAAAAAAAAAAA */ 1090785345, /* AACAACAACAACAACAAC */ 2181570690, /* AAGAAGAAGAAGAAGAAG */ 3272356035, /* AATAATAATAATAATAAT */ 4363141380, /* ACAACAACAACAACAACA */ 4581298449, /* ACACACACACACACACAC */ 5453926725, /* ACCACCACCACCACCACC */ 6544712070, /* ACGACGACGACGACGACG */ 7635497415, /* ACTACTACTACTACTACT */ 8726282760, /* AGAAGAAGAAGAAGAAGA */ 9162596898, /* AGAGAGAGAGAGAGAGAG */ 9817068105, /* AGCAGCAGCAGCAGCAGC */ 10907853450, /* AGGAGGAGGAGGAGGAGG */ 11998638795, /* AGTAGTAGTAGTAGTAGT */ 13089424140, /* ATAATAATAATAATAATA */ 13743895347, /* ATATATATATATATATAT */ 14180209485, /* ATCATCATCATCATCATC */ 15270994830, /* ATGATGATGATGATGATG */ 16361780175, /* ATTATTATTATTATTATT */ 17452565520, /* CAACAACAACAACAACAA */ 18325193796, /* CACACACACACACACACA */ 18543350865, /* CACCACCACCACCACCAC */ 19634136210, /* CAGCAGCAGCAGCAGCAG */ 20724921555, /* CATCATCATCATCATCAT */ 21815706900, /* CCACCACCACCACCACCA */ 22906492245, /* CCCCCCCCCCCCCCCCCC */ 23997277590, /* CCGCCGCCGCCGCCGCCG */ 25088062935, /* CCTCCTCCTCCTCCTCCT */ 26178848280, /* CGACGACGACGACGACGA */ 27269633625, /* CGCCGCCGCCGCCGCCGC */ 27487790694, /* CGCGCGCGCGCGCGCGCG */ 28360418970, /* CGGCGGCGGCGGCGGCGG */ 29451204315, /* CGTCGTCGTCGTCGTCGT */ 30541989660, /* CTACTACTACTACTACTA */ 31632775005, /* CTCCTCCTCCTCCTCCTC */ 32069089143, /* CTCTCTCTCTCTCTCTCT */ 32723560350, /* CTGCTGCTGCTGCTGCTG */ 33814345695, /* CTTCTTCTTCTTCTTCTT */ 34905131040, /* GAAGAAGAAGAAGAAGAA */ 35995916385, /* GACGACGACGACGACGAC */ 36650387592, /* GAGAGAGAGAGAGAGAGA */ 37086701730, /* GAGGAGGAGGAGGAGGAG */ 38177487075, /* GATGATGATGATGATGAT */ 39268272420, /* GCAGCAGCAGCAGCAGCA */ 40359057765, /* GCCGCCGCCGCCGCCGCC */ 41231686041, /* GCGCGCGCGCGCGCGCGC */ 41449843110, /* GCGGCGGCGGCGGCGGCG */ 42540628455, /* GCTGCTGCTGCTGCTGCT */ 43631413800, /* GGAGGAGGAGGAGGAGGA */ 44722199145, /* GGCGGCGGCGGCGGCGGC */ 45812984490, /* GGGGGGGGGGGGGGGGGG */ 46903769835, /* GGTGGTGGTGGTGGTGGT */ 47994555180, /* GTAGTAGTAGTAGTAGTA */ 49085340525, /* GTCGTCGTCGTCGTCGTC */ 50176125870, /* GTGGTGGTGGTGGTGGTG */ 50394282939, /* GTGTGTGTGTGTGTGTGT */ 51266911215, /* GTTGTTGTTGTTGTTGTT */ 52357696560, /* TAATAATAATAATAATAA */ 53448481905, /* TACTACTACTACTACTAC */ 54539267250, /* TAGTAGTAGTAGTAGTAG */ 54975581388, /* TATATATATATATATATA */ 55630052595, /* TATTATTATTATTATTAT */ 56720837940, /* TCATCATCATCATCATCA */ 57811623285, /* TCCTCCTCCTCCTCCTCC */ 58902408630, /* TCGTCGTCGTCGTCGTCG */ 59556879837, /* TCTCTCTCTCTCTCTCTC */ 59993193975, /* TCTTCTTCTTCTTCTTCT */ 61083979320, /* TGATGATGATGATGATGA */ 62174764665, /* TGCTGCTGCTGCTGCTGC */ 63265550010, /* TGGTGGTGGTGGTGGTGG */ 64138178286, /* TGTGTGTGTGTGTGTGTG */ 64356335355, /* TGTTGTTGTTGTTGTTGT */ 65447120700, /* TTATTATTATTATTATTA */ 66537906045, /* TTCTTCTTCTTCTTCTTC */ 67628691390, /* TTGTTGTTGTTGTTGTTG */ 68719476735, /* TTTTTTTTTTTTTTTTTT */ }; static Oligospace_T repetitive_oligos_19[NREPETITIVE] = {0, /* AAAAAAAAAAAAAAAAAAA */ 4363141380, /* AACAACAACAACAACAACA */ 8726282760, /* AAGAAGAAGAAGAAGAAGA */ 13089424140, /* AATAATAATAATAATAATA */ 17452565520, /* ACAACAACAACAACAACAA */ 18325193796, /* ACACACACACACACACACA */ 21815706900, /* ACCACCACCACCACCACCA */ 26178848280, /* ACGACGACGACGACGACGA */ 30541989660, /* ACTACTACTACTACTACTA */ 34905131040, /* AGAAGAAGAAGAAGAAGAA */ 36650387592, /* AGAGAGAGAGAGAGAGAGA */ 39268272420, /* AGCAGCAGCAGCAGCAGCA */ 43631413800, /* AGGAGGAGGAGGAGGAGGA */ 47994555180, /* AGTAGTAGTAGTAGTAGTA */ 52357696560, /* ATAATAATAATAATAATAA */ 54975581388, /* ATATATATATATATATATA */ 56720837940, /* ATCATCATCATCATCATCA */ 61083979320, /* ATGATGATGATGATGATGA */ 65447120700, /* ATTATTATTATTATTATTA */ 69810262081, /* CAACAACAACAACAACAAC */ 73300775185, /* CACACACACACACACACAC */ 74173403461, /* CACCACCACCACCACCACC */ 78536544841, /* CAGCAGCAGCAGCAGCAGC */ 82899686221, /* CATCATCATCATCATCATC */ 87262827601, /* CCACCACCACCACCACCAC */ 91625968981, /* CCCCCCCCCCCCCCCCCCC */ 95989110361, /* CCGCCGCCGCCGCCGCCGC */ 100352251741, /* CCTCCTCCTCCTCCTCCTC */ 104715393121, /* CGACGACGACGACGACGAC */ 109078534501, /* CGCCGCCGCCGCCGCCGCC */ 109951162777, /* CGCGCGCGCGCGCGCGCGC */ 113441675881, /* CGGCGGCGGCGGCGGCGGC */ 117804817261, /* CGTCGTCGTCGTCGTCGTC */ 122167958641, /* CTACTACTACTACTACTAC */ 126531100021, /* CTCCTCCTCCTCCTCCTCC */ 128276356573, /* CTCTCTCTCTCTCTCTCTC */ 130894241401, /* CTGCTGCTGCTGCTGCTGC */ 135257382781, /* CTTCTTCTTCTTCTTCTTC */ 139620524162, /* GAAGAAGAAGAAGAAGAAG */ 143983665542, /* GACGACGACGACGACGACG */ 146601550370, /* GAGAGAGAGAGAGAGAGAG */ 148346806922, /* GAGGAGGAGGAGGAGGAGG */ 152709948302, /* GATGATGATGATGATGATG */ 157073089682, /* GCAGCAGCAGCAGCAGCAG */ 161436231062, /* GCCGCCGCCGCCGCCGCCG */ 164926744166, /* GCGCGCGCGCGCGCGCGCG */ 165799372442, /* GCGGCGGCGGCGGCGGCGG */ 170162513822, /* GCTGCTGCTGCTGCTGCTG */ 174525655202, /* GGAGGAGGAGGAGGAGGAG */ 178888796582, /* GGCGGCGGCGGCGGCGGCG */ 183251937962, /* GGGGGGGGGGGGGGGGGGG */ 187615079342, /* GGTGGTGGTGGTGGTGGTG */ 191978220722, /* GTAGTAGTAGTAGTAGTAG */ 196341362102, /* GTCGTCGTCGTCGTCGTCG */ 200704503482, /* GTGGTGGTGGTGGTGGTGG */ 201577131758, /* GTGTGTGTGTGTGTGTGTG */ 205067644862, /* GTTGTTGTTGTTGTTGTTG */ 209430786243, /* TAATAATAATAATAATAAT */ 213793927623, /* TACTACTACTACTACTACT */ 218157069003, /* TAGTAGTAGTAGTAGTAGT */ 219902325555, /* TATATATATATATATATAT */ 222520210383, /* TATTATTATTATTATTATT */ 226883351763, /* TCATCATCATCATCATCAT */ 231246493143, /* TCCTCCTCCTCCTCCTCCT */ 235609634523, /* TCGTCGTCGTCGTCGTCGT */ 238227519351, /* TCTCTCTCTCTCTCTCTCT */ 239972775903, /* TCTTCTTCTTCTTCTTCTT */ 244335917283, /* TGATGATGATGATGATGAT */ 248699058663, /* TGCTGCTGCTGCTGCTGCT */ 253062200043, /* TGGTGGTGGTGGTGGTGGT */ 256552713147, /* TGTGTGTGTGTGTGTGTGT */ 257425341423, /* TGTTGTTGTTGTTGTTGTT */ 261788482803, /* TTATTATTATTATTATTAT */ 266151624183, /* TTCTTCTTCTTCTTCTTCT */ 270514765563, /* TTGTTGTTGTTGTTGTTGT */ 274877906943, /* TTTTTTTTTTTTTTTTTTT */ }; static Oligospace_T repetitive_oligos_20[NREPETITIVE] = {0, /* AAAAAAAAAAAAAAAAAAAA */ 17452565520, /* AACAACAACAACAACAACAA */ 34905131040, /* AAGAAGAAGAAGAAGAAGAA */ 52357696560, /* AATAATAATAATAATAATAA */ 69810262081, /* ACAACAACAACAACAACAAC */ 73300775185, /* ACACACACACACACACACAC */ 87262827601, /* ACCACCACCACCACCACCAC */ 104715393121, /* ACGACGACGACGACGACGAC */ 122167958641, /* ACTACTACTACTACTACTAC */ 139620524162, /* AGAAGAAGAAGAAGAAGAAG */ 146601550370, /* AGAGAGAGAGAGAGAGAGAG */ 157073089682, /* AGCAGCAGCAGCAGCAGCAG */ 174525655202, /* AGGAGGAGGAGGAGGAGGAG */ 191978220722, /* AGTAGTAGTAGTAGTAGTAG */ 209430786243, /* ATAATAATAATAATAATAAT */ 219902325555, /* ATATATATATATATATATAT */ 226883351763, /* ATCATCATCATCATCATCAT */ 244335917283, /* ATGATGATGATGATGATGAT */ 261788482803, /* ATTATTATTATTATTATTAT */ 279241048324, /* CAACAACAACAACAACAACA */ 293203100740, /* CACACACACACACACACACA */ 296693613844, /* CACCACCACCACCACCACCA */ 314146179364, /* CAGCAGCAGCAGCAGCAGCA */ 331598744884, /* CATCATCATCATCATCATCA */ 349051310405, /* CCACCACCACCACCACCACC */ 366503875925, /* CCCCCCCCCCCCCCCCCCCC */ 383956441445, /* CCGCCGCCGCCGCCGCCGCC */ 401409006965, /* CCTCCTCCTCCTCCTCCTCC */ 418861572486, /* CGACGACGACGACGACGACG */ 436314138006, /* CGCCGCCGCCGCCGCCGCCG */ 439804651110, /* CGCGCGCGCGCGCGCGCGCG */ 453766703526, /* CGGCGGCGGCGGCGGCGGCG */ 471219269046, /* CGTCGTCGTCGTCGTCGTCG */ 488671834567, /* CTACTACTACTACTACTACT */ 506124400087, /* CTCCTCCTCCTCCTCCTCCT */ 513105426295, /* CTCTCTCTCTCTCTCTCTCT */ 523576965607, /* CTGCTGCTGCTGCTGCTGCT */ 541029531127, /* CTTCTTCTTCTTCTTCTTCT */ 558482096648, /* GAAGAAGAAGAAGAAGAAGA */ 575934662168, /* GACGACGACGACGACGACGA */ 586406201480, /* GAGAGAGAGAGAGAGAGAGA */ 593387227688, /* GAGGAGGAGGAGGAGGAGGA */ 610839793208, /* GATGATGATGATGATGATGA */ 628292358729, /* GCAGCAGCAGCAGCAGCAGC */ 645744924249, /* GCCGCCGCCGCCGCCGCCGC */ 659706976665, /* GCGCGCGCGCGCGCGCGCGC */ 663197489769, /* GCGGCGGCGGCGGCGGCGGC */ 680650055289, /* GCTGCTGCTGCTGCTGCTGC */ 698102620810, /* GGAGGAGGAGGAGGAGGAGG */ 715555186330, /* GGCGGCGGCGGCGGCGGCGG */ 733007751850, /* GGGGGGGGGGGGGGGGGGGG */ 750460317370, /* GGTGGTGGTGGTGGTGGTGG */ 767912882891, /* GTAGTAGTAGTAGTAGTAGT */ 785365448411, /* GTCGTCGTCGTCGTCGTCGT */ 802818013931, /* GTGGTGGTGGTGGTGGTGGT */ 806308527035, /* GTGTGTGTGTGTGTGTGTGT */ 820270579451, /* GTTGTTGTTGTTGTTGTTGT */ 837723144972, /* TAATAATAATAATAATAATA */ 855175710492, /* TACTACTACTACTACTACTA */ 872628276012, /* TAGTAGTAGTAGTAGTAGTA */ 879609302220, /* TATATATATATATATATATA */ 890080841532, /* TATTATTATTATTATTATTA */ 907533407053, /* TCATCATCATCATCATCATC */ 924985972573, /* TCCTCCTCCTCCTCCTCCTC */ 942438538093, /* TCGTCGTCGTCGTCGTCGTC */ 952910077405, /* TCTCTCTCTCTCTCTCTCTC */ 959891103613, /* TCTTCTTCTTCTTCTTCTTC */ 977343669134, /* TGATGATGATGATGATGATG */ 994796234654, /* TGCTGCTGCTGCTGCTGCTG */ 1012248800174, /* TGGTGGTGGTGGTGGTGGTG */ 1026210852590, /* TGTGTGTGTGTGTGTGTGTG */ 1029701365694, /* TGTTGTTGTTGTTGTTGTTG */ 1047153931215, /* TTATTATTATTATTATTATT */ 1064606496735, /* TTCTTCTTCTTCTTCTTCTT */ 1082059062255, /* TTGTTGTTGTTGTTGTTGTT */ 1099511627775, /* TTTTTTTTTTTTTTTTTTTT */ }; #if 0 #define ALL_NREPETITIVE 4336 static Storedoligomer_T all_repetitive_oligos[ALL_NREPETITIVE] = { 0, 4097, 8194, 12291, 16388, 20485, 24582, 28679, 32776, 36873, 40970, 45067, 49164, 53261, 57358, 61455, 65552, 65793, 69649, 73746, 77843, 81940, 86037, 90134, 94231, 98328, 102425, 106522, 110619, 114716, 118813, 122910, 127007, 131104, 131586, 135201, 139298, 143395, 147492, 151589, 155686, 159783, 163880, 167977, 172074, 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12942423,12946520,12950617,12954714,12958811,12961221,12962908,12967005, 12971102,12975199,12979296,12983393,12987490,12991587,12995684,12999781, 13003878,13007975,13012072,13016169,13020266,13024363,13027014,13028460, 13032557,13036654,13040751,13044848,13048945,13053042,13057139,13061236, 13065333,13069430,13073527,13077624,13081721,13085818,13089915,13092807, 13094012,13098109,13102206,13106303,13110400,13114497,13118594,13122691, 13126788,13130885,13134982,13139079,13143176,13147273,13151370,13155467, 13158600,13159564,13163661,13167758,13171855,13175952,13180049,13184146, 13188243,13192340,13196437,13200534,13204631,13208728,13212825,13216922, 13221019,13224393,13225116,13229213,13233310,13237407,13241504,13245601, 13249698,13253795,13257892,13261989,13266086,13270183,13274280,13278377, 13282474,13286571,13290186,13290668,13294765,13298862,13302959,13307056, 13311153,13315250,13319347,13323444,13327541,13331638,13335735,13339832, 13343929,13348026,13352123,13355979,13356220,13360317,13364414,13368511, 13372608,13376705,13380802,13384899,13388996,13393093,13397190,13401287, 13405384,13409481,13413578,13417675,13421772,13425869,13429966,13434063, 13438160,13442257,13446354,13450451,13454548,13458645,13462742,13466839, 13470936,13475033,13479130,13483227,13487324,13487565,13491421,13495518, 13499615,13503712,13507809,13511906,13516003,13520100,13524197,13528294, 13532391,13536488,13540585,13544682,13548779,13552876,13553358,13556973, 13561070,13565167,13569264,13573361,13577458,13581555,13585652,13589749, 13593846,13597943,13602040,13606137,13610234,13614331,13618428,13619151, 13622525,13626622,13630719,13634816,13638913,13643010,13647107,13651204, 13655301,13659398,13663495,13667592,13671689,13675786,13679883,13683980, 13684944,13688077,13692174,13696271,13700368,13704465,13708562,13712659, 13716756,13720853,13724950,13729047,13733144,13737241,13741338,13745435, 13749532,13750737,13753629,13757726,13761823,13765920,13770017,13774114, 13778211,13782308,13786405,13790502,13794599,13798696,13802793,13806890, 13810987,13815084,13816530,13819181,13823278,13827375,13831472,13835569, 13839666,13843763,13847860,13851957,13856054,13860151,13864248,13868345, 13872442,13876539,13880636,13882323,13884733,13888830,13892927,13897024, 13901121,13905218,13909315,13913412,13917509,13921606,13925703,13929800, 13933897,13937994,13942091,13946188,13948116,13950285,13954382,13958479, 13962576,13966673,13970770,13974867,13978964,13983061,13987158,13991255, 13995352,13999449,14003546,14007643,14011740,14013909,14015837,14019934, 14024031,14028128,14032225,14036322,14040419,14044516,14048613,14052710, 14056807,14060904,14065001,14069098,14073195,14077292,14079702,14081389, 14085486,14089583,14093680,14097777,14101874,14105971,14110068,14114165, 14118262,14122359,14126456,14130553,14134650,14138747,14142844,14145495, 14146941,14151038,14155135,14159232,14163329,14167426,14171523,14175620, 14179717,14183814,14187911,14192008,14196105,14200202,14204299,14208396, 14211288,14212493,14216590,14220687,14224784,14228881,14232978,14237075, 14241172,14245269,14249366,14253463,14257560,14261657,14265754,14269851, 14273948,14277081,14278045,14282142,14286239,14290336,14294433,14298530, 14302627,14306724,14310821,14314918,14319015,14323112,14327209,14331306, 14335403,14339500,14342874,14343597,14347694,14351791,14355888,14359985, 14364082,14368179,14372276,14376373,14380470,14384567,14388664,14392761, 14396858,14400955,14405052,14408667,14409149,14413246,14417343,14421440, 14425537,14429634,14433731,14437828,14441925,14446022,14450119,14454216, 14458313,14462410,14466507,14470604,14474460,14474701,14478798,14482895, 14486992,14491089,14495186,14499283,14503380,14507477,14511574,14515671, 14519768,14523865,14527962,14532059,14536156,14540253,14544350,14548447, 14552544,14556641,14560738,14564835,14568932,14573029,14577126,14581223, 14585320,14589417,14593514,14597611,14601708,14605805,14606046,14609902, 14613999,14618096,14622193,14626290,14630387,14634484,14638581,14642678, 14646775,14650872,14654969,14659066,14663163,14667260,14671357,14671839, 14675454,14679551,14683648,14687745,14691842,14695939,14700036,14704133, 14708230,14712327,14716424,14720521,14724618,14728715,14732812,14736909, 14737632,14741006,14745103,14749200,14753297,14757394,14761491,14765588, 14769685,14773782,14777879,14781976,14786073,14790170,14794267,14798364, 14802461,14803425,14806558,14810655,14814752,14818849,14822946,14827043, 14831140,14835237,14839334,14843431,14847528,14851625,14855722,14859819, 14863916,14868013,14869218,14872110,14876207,14880304,14884401,14888498, 14892595,14896692,14900789,14904886,14908983,14913080,14917177,14921274, 14925371,14929468,14933565,14935011,14937662,14941759,14945856,14949953, 14954050,14958147,14962244,14966341,14970438,14974535,14978632,14982729, 14986826,14990923,14995020,14999117,15000804,15003214,15007311,15011408, 15015505,15019602,15023699,15027796,15031893,15035990,15040087,15044184, 15048281,15052378,15056475,15060572,15064669,15066597,15068766,15072863, 15076960,15081057,15085154,15089251,15093348,15097445,15101542,15105639, 15109736,15113833,15117930,15122027,15126124,15130221,15132390,15134318, 15138415,15142512,15146609,15150706,15154803,15158900,15162997,15167094, 15171191,15175288,15179385,15183482,15187579,15191676,15195773,15198183, 15199870,15203967,15208064,15212161,15216258,15220355,15224452,15228549, 15232646,15236743,15240840,15244937,15249034,15253131,15257228,15261325, 15263976,15265422,15269519,15273616,15277713,15281810,15285907,15290004, 15294101,15298198,15302295,15306392,15310489,15314586,15318683,15322780, 15326877,15329769,15330974,15335071,15339168,15343265,15347362,15351459, 15355556,15359653,15363750,15367847,15371944,15376041,15380138,15384235, 15388332,15392429,15395562,15396526,15400623,15404720,15408817,15412914, 15417011,15421108,15425205,15429302,15433399,15437496,15441593,15445690, 15449787,15453884,15457981,15461355,15462078,15466175,15470272,15474369, 15478466,15482563,15486660,15490757,15494854,15498951,15503048,15507145, 15511242,15515339,15519436,15523533,15527148,15527630,15531727,15535824, 15539921,15544018,15548115,15552212,15556309,15560406,15564503,15568600, 15572697,15576794,15580891,15584988,15589085,15592941,15593182,15597279, 15601376,15605473,15609570,15613667,15617764,15621861,15625958,15630055, 15634152,15638249,15642346,15646443,15650540,15654637,15658734,15662831, 15666928,15671025,15675122,15679219,15683316,15687413,15691510,15695607, 15699704,15703801,15707898,15711995,15716092,15720189,15724286,15724527, 15728383,15732480,15736577,15740674,15744771,15748868,15752965,15757062, 15761159,15765256,15769353,15773450,15777547,15781644,15785741,15789838, 15790320,15793935,15798032,15802129,15806226,15810323,15814420,15818517, 15822614,15826711,15830808,15834905,15839002,15843099,15847196,15851293, 15855390,15856113,15859487,15863584,15867681,15871778,15875875,15879972, 15884069,15888166,15892263,15896360,15900457,15904554,15908651,15912748, 15916845,15920942,15921906,15925039,15929136,15933233,15937330,15941427, 15945524,15949621,15953718,15957815,15961912,15966009,15970106,15974203, 15978300,15982397,15986494,15987699,15990591,15994688,15998785,16002882, 16006979,16011076,16015173,16019270,16023367,16027464,16031561,16035658, 16039755,16043852,16047949,16052046,16053492,16056143,16060240,16064337, 16068434,16072531,16076628,16080725,16084822,16088919,16093016,16097113, 16101210,16105307,16109404,16113501,16117598,16119285,16121695,16125792, 16129889,16133986,16138083,16142180,16146277,16150374,16154471,16158568, 16162665,16166762,16170859,16174956,16179053,16183150,16185078,16187247, 16191344,16195441,16199538,16203635,16207732,16211829,16215926,16220023, 16224120,16228217,16232314,16236411,16240508,16244605,16248702,16250871, 16252799,16256896,16260993,16265090,16269187,16273284,16277381,16281478, 16285575,16289672,16293769,16297866,16301963,16306060,16310157,16314254, 16316664,16318351,16322448,16326545,16330642,16334739,16338836,16342933, 16347030,16351127,16355224,16359321,16363418,16367515,16371612,16375709, 16379806,16382457,16383903,16388000,16392097,16396194,16400291,16404388, 16408485,16412582,16416679,16420776,16424873,16428970,16433067,16437164, 16441261,16445358,16448250,16449455,16453552,16457649,16461746,16465843, 16469940,16474037,16478134,16482231,16486328,16490425,16494522,16498619, 16502716,16506813,16510910,16514043,16515007,16519104,16523201,16527298, 16531395,16535492,16539589,16543686,16547783,16551880,16555977,16560074, 16564171,16568268,16572365,16576462,16579836,16580559,16584656,16588753, 16592850,16596947,16601044,16605141,16609238,16613335,16617432,16621529, 16625626,16629723,16633820,16637917,16642014,16645629,16646111,16650208, 16654305,16658402,16662499,16666596,16670693,16674790,16678887,16682984, 16687081,16691178,16695275,16699372,16703469,16707566,16711422,16711663, 16715760,16719857,16723954,16728051,16732148,16736245,16740342,16744439, 16748536,16752633,16756730,16760827,16764924,16769021,16773118,16777215, }; #endif static int oligosize; static Oligospace_T *repetitive_oligos; void Oligo_setup (int index1part) { oligosize = index1part; if (index1part == 6) { repetitive_oligos = repetitive_oligos_6; } else if (index1part == 7) { repetitive_oligos = repetitive_oligos_7; } else if (index1part == 8) { repetitive_oligos = repetitive_oligos_8; } else if (index1part == 9) { repetitive_oligos = repetitive_oligos_9; } else if (index1part == 10) { repetitive_oligos = repetitive_oligos_10; } else if (index1part == 11) { repetitive_oligos = repetitive_oligos_11; } else if (index1part == 12) { repetitive_oligos = repetitive_oligos_12; } else if (index1part == 13) { repetitive_oligos = repetitive_oligos_13; } else if (index1part == 14) { repetitive_oligos = repetitive_oligos_14; } else if (index1part == 15) { repetitive_oligos = repetitive_oligos_15; } else if (index1part == 16) { repetitive_oligos = repetitive_oligos_16; } else if (index1part == 17) { repetitive_oligos = repetitive_oligos_17; } else if (index1part == 18) { repetitive_oligos = repetitive_oligos_18; } else if (index1part == 19) { repetitive_oligos = repetitive_oligos_19; } else if (index1part == 20) { repetitive_oligos = repetitive_oligos_20; } else { fprintf(stderr,"Oligo_setup can handle only values of 6 through 20\n"); abort(); } return; } /************************************************************************ * Check ************************************************************************/ /* 87654321 */ #define LOW_TWO_BITS 0x00000003 /* For debugging purposes only */ char * Oligo_one_nt (Oligospace_T oligo, int oligosize) { char *nt; int i, j; Oligospace_T lowbits; nt = (char *) CALLOC(oligosize+1,sizeof(char)); j = oligosize-1; for (i = 0; i < oligosize; i++) { lowbits = oligo & LOW_TWO_BITS; switch (lowbits) { case RIGHT_A: nt[j] = 'A'; break; case RIGHT_C: nt[j] = 'C'; break; case RIGHT_G: nt[j] = 'G'; break; case RIGHT_T: nt[j] = 'T'; break; } oligo >>= 2; j--; } return nt; } /* This procedure is called only by GMAP. If characters are pushed onto left end, oligo will need to be shifted beforehand. Note: positions is allocated by system malloc() */ /* No longer seems to be called by GMAP either */ int Oligo_lookup (Univcoord_T **positions, Indexdb_T indexdb, Oligospace_T storedoligo) { int nentries; debug(char *nt); debug1(int i); debug(nt = Oligo_one_nt(storedoligo,16); printf("Oligo on entry = %06X (%s)",storedoligo,nt); FREE(nt); ); if ((*positions = Indexdb_read(&nentries,indexdb,storedoligo)) == NULL) { debug(printf(" not found\n")); return 0; } else { debug(printf(" => %d entries: ",nentries)); debug1( for (i = 0; i < nentries; i++) { printf("%u ",(*positions)[i]); } printf("\n"); ); debug(printf("\n")); return nentries; } } static Oligostate_T oligo_read (int *querypos, Oligospace_T *forward, Oligospace_T *revcomp, Reader_T reader, cDNAEnd_T cdnaend) { int count = 0; int c; *forward = *revcomp = 0U; if (cdnaend == FIVE) { while (count < oligosize && (c = Reader_getc(reader,cdnaend)) != '\0') { switch (c) { case 'A': *forward <<= 2; *revcomp >>= 2; *revcomp |= LEFT_T; break; case 'C': *forward <<= 2; *forward |= RIGHT_C; *revcomp >>= 2; *revcomp |= LEFT_G; break; case 'G': *forward <<= 2; *forward |= RIGHT_G; *revcomp >>= 2; *revcomp |= LEFT_C; break; case 'T': *forward <<= 2; *forward |= RIGHT_T; *revcomp >>= 2; break; default: *forward = *revcomp = 0U; count = -1; /* This counteracts count++ below */ } count++; debug(printf("5' Read %c, count = %d, oligo = %06X, %06X\n", c,count,*forward,*revcomp)); } } else { while (count < oligosize && (c = Reader_getc(reader,cdnaend)) != '\0') { switch (c) { case 'A': *forward >>= 2; *revcomp <<= 2; *revcomp |= RIGHT_T; break; case 'C': *forward >>= 2; *forward |= LEFT_C; *revcomp <<= 2; *revcomp |= RIGHT_G; break; case 'G': *forward >>= 2; *forward |= LEFT_G; *revcomp <<= 2; *revcomp |= RIGHT_C; break; case 'T': *forward >>= 2; *forward |= LEFT_T; *revcomp <<= 2; break; default: *forward = *revcomp = 0U; count = -1; /* This counteracts count++ below */ } count++; debug(printf("3' Read %c, count = %d, oligo = %06X, %06X\n", c,count,*forward,*revcomp)); } } if (count < oligosize) { *forward = *revcomp = 0U; return DONE; } else { debug(printf("Read: Returning oligo %06X for count = %d and size = %d\n", *forward,count,oligosize)); if (cdnaend == FIVE) { *querypos = Reader_startpos(reader) - oligosize; debug(printf("Setting querypos to be %u - %u = %u\n", Reader_startpos(reader),oligosize,*querypos)); } else { *querypos = Reader_endpos(reader) + 1; debug(printf("Setting querypos to be %u + 1 = %u\n", Reader_endpos(reader),*querypos)); } return VALID; } } #if 0 static Oligostate_T oligo_read_dibase (int *querypos, Oligospace_T *forward, Oligospace_T *revcomp, Reader_T reader, cDNAEnd_T cdnaend) { int count = 0; int c; *forward = *revcomp = 0U; if (cdnaend == FIVE) { while (count < oligosize && (c = Reader_getc(reader,cdnaend)) != '\0') { switch (c) { case '0': *forward <<= 2; *revcomp >>= 2; break; case '1': *forward <<= 2; *forward |= RIGHT_1; *revcomp >>= 2; *revcomp |= LEFT_1; break; case '2': *forward <<= 2; *forward |= RIGHT_2; *revcomp >>= 2; *revcomp |= LEFT_2; break; case '3': *forward <<= 2; *forward |= RIGHT_3; *revcomp >>= 2; *revcomp |= LEFT_3; break; default: *forward = *revcomp = 0U; count = -1; /* This counteracts count++ below */ } count++; debug(printf("5' Read %c, count = %d, oligo = %06X, %06X\n", c,count,*forward,*revcomp)); } } else { while (count < oligosize && (c = Reader_getc(reader,cdnaend)) != '\0') { switch (c) { case '0': *forward >>= 2; *revcomp <<= 2; break; case '1': *forward >>= 2; *forward |= LEFT_1; *revcomp <<= 2; *revcomp |= RIGHT_1; break; case '2': *forward >>= 2; *forward |= LEFT_2; *revcomp <<= 2; *revcomp |= RIGHT_2; break; case '3': *forward >>= 2; *forward |= LEFT_3; *revcomp <<= 2; *revcomp |= RIGHT_3; break; default: *forward = *revcomp = 0U; count = -1; /* This counteracts count++ below */ } count++; debug(printf("3' Read %c, count = %d, oligo = %06X, %06X\n", c,count,*forward,*revcomp)); } } if (count < oligosize) { *forward = *revcomp = 0U; return DONE; } else { debug(printf("Read: Returning oligo %06X for count = %d and size = %d\n", *forward,count,oligosize)); if (cdnaend == FIVE) { *querypos = Reader_startpos(reader) - oligosize; debug(printf("Setting querypos to be %u - %u = %u\n", Reader_startpos(reader),oligosize,*querypos)); } else { *querypos = Reader_endpos(reader) + 1; debug(printf("Setting querypos to be %u + 1 = %u\n", Reader_endpos(reader),*querypos)); } return VALID; } } #endif #if 0 typedef Oligostate_T (*oligo_read_proc_t) (int *, Oligospace_T *, Oligospace_T *, int, Reader_T, cDNAEnd_T); static oligo_read_proc_t oligo_read; #endif static Oligostate_T oligo_revise (int *querypos, Oligospace_T *forward, Oligospace_T *revcomp, Reader_T reader, cDNAEnd_T cdnaend) { char c; if ((c = Reader_getc(reader,cdnaend)) == '\0') { *forward = *revcomp = 0U; debug( if (cdnaend == FIVE) { printf("5' Revision: read terminating char '0'\n"); } else { printf("3' Revision: read terminating char '0'\n"); } ); return DONE; } else if (cdnaend == FIVE) { switch (c) { case 'A': *forward <<= 2; *revcomp >>= 2; *revcomp |= LEFT_T; break; case 'C': *forward <<= 2; *forward |= RIGHT_C; *revcomp >>= 2; *revcomp |= LEFT_G; break; case 'G': *forward <<= 2; *forward |= RIGHT_G; *revcomp >>= 2; *revcomp |= LEFT_C; break; case 'T': *forward <<= 2; *forward |= RIGHT_T; *revcomp >>= 2; break; default: *forward = *revcomp = 0U; *querypos = Reader_startpos(reader) - oligosize; return INVALID; } *querypos = Reader_startpos(reader) - oligosize; debug(printf("5' Revision: read char %c, oligo = %06X, %06X at querypos %d\n", c,*forward,*revcomp,*querypos)); return VALID; } else { switch (c) { case 'A': *forward >>= 2; *revcomp <<= 2; *revcomp |= RIGHT_T; break; case 'C': *forward >>= 2; *forward |= LEFT_C; *revcomp <<= 2; *revcomp |= RIGHT_G; break; case 'G': *forward >>= 2; *forward |= LEFT_G; *revcomp <<= 2; *revcomp |= RIGHT_C; break; case 'T': *forward >>= 2; *forward |= LEFT_T; *revcomp <<= 2; break; default: *forward = *revcomp = 0U; *querypos = Reader_endpos(reader) + 1; return INVALID; } *querypos = Reader_endpos(reader) + 1; debug(printf("3' Revision: read char %c, oligo = %06X, %06X at querypos %d\n", c,*forward,*revcomp,*querypos)); return VALID; } } #if 0 static Oligostate_T oligo_revise_dibase (int *querypos, Oligospace_T *forward, Oligospace_T *revcomp, Reader_T reader, cDNAEnd_T cdnaend) { char c; if ((c = Reader_getc(reader,cdnaend)) == '\0') { *forward = *revcomp = 0U; debug( if (cdnaend == FIVE) { printf("5' Revision: read terminating char '0'\n"); } else { printf("3' Revision: read terminating char '0'\n"); } ); return DONE; } else if (cdnaend == FIVE) { switch (c) { case '0': *forward <<= 2; *revcomp >>= 2; break; case '1': *forward <<= 2; *forward |= RIGHT_1; *revcomp >>= 2; *revcomp |= LEFT_1; break; case '2': *forward <<= 2; *forward |= RIGHT_2; *revcomp >>= 2; *revcomp |= LEFT_2; break; case '3': *forward <<= 2; *forward |= RIGHT_3; *revcomp >>= 2; *revcomp |= LEFT_3; break; default: *forward = *revcomp = 0U; *querypos = Reader_startpos(reader) - oligosize; return INVALID; } *querypos = Reader_startpos(reader) - oligosize; debug(printf("5' Revision: read char %c, oligo = %06X, %06X at querypos %d\n", c,*forward,*revcomp,*querypos)); return VALID; } else { switch (c) { case '0': *forward >>= 2; *revcomp <<= 2; break; case '1': *forward >>= 2; *forward |= LEFT_1; *revcomp <<= 2; *revcomp |= RIGHT_1; break; case '2': *forward >>= 2; *forward |= LEFT_2; *revcomp <<= 2; *revcomp |= RIGHT_2; break; case '3': *forward >>= 2; *forward |= LEFT_3; *revcomp <<= 2; *revcomp |= RIGHT_3; break; default: *forward = *revcomp = 0U; *querypos = Reader_endpos(reader) + 1; return INVALID; } *querypos = Reader_endpos(reader) + 1; debug(printf("3' Revision: read char %c, oligo = %06X, %06X at querypos %d\n", c,*forward,*revcomp,*querypos)); return VALID; } } #endif #if 0 typedef Oligostate_T (*oligo_revise_proc_t) (int *, Oligospace_T *, Oligospace_T *, int, Reader_T, cDNAEnd_T); static oligo_revise_proc_t oligo_revise; #endif Oligostate_T Oligo_next (Oligostate_T last_state, int *querypos, Oligospace_T *forward, Oligospace_T *revcomp, Reader_T reader, cDNAEnd_T cdnaend) { Oligostate_T state; if (last_state == DONE) { fprintf(stderr,"Called Oligo_next with last_state == DONE\n"); exit(1); } else if (last_state == VALID) { if ((state = oligo_revise(&(*querypos),&(*forward),&(*revcomp),reader,cdnaend)) == DONE) { return DONE; } else if (state == VALID) { return VALID; } else { /* state == INVALID */ return oligo_read(&(*querypos),&(*forward),&(*revcomp),reader,cdnaend); } } else { /* INVALID and INIT */ return oligo_read(&(*querypos),&(*forward),&(*revcomp),reader,cdnaend); } } Oligostate_T Oligo_skip (Oligostate_T last_state, int *querypos, Oligospace_T *forward, Oligospace_T *revcomp, Reader_T reader, cDNAEnd_T cdnaend, int nskip) { int i = 0; while (i < nskip && last_state != DONE) { if (last_state == VALID) { last_state = oligo_revise(&(*querypos),&(*forward),&(*revcomp),reader,cdnaend); i++; } else { /* INVALID and INIT */ last_state = oligo_read(&(*querypos),&(*forward),&(*revcomp),reader,cdnaend); i += oligosize; } } return last_state; } #if 0 /* Procedure used by oligo-count.c. oligosize here is expected to be > 12. */ char * Oligo_nt (Oligospace_T oligo1, Oligospace_T oligo2, int oligosize, int index1part) { char *nt; int i, j; Oligospace_T lowbits; nt = (char *) CALLOC(oligosize+1,sizeof(char)); j = oligosize-1; for (i = 0; i < oligosize - index1part; i++) { lowbits = oligo2 & LOW_TWO_BITS; switch (lowbits) { case RIGHT_A: nt[j] = 'A'; break; case RIGHT_C: nt[j] = 'C'; break; case RIGHT_G: nt[j] = 'G'; break; case RIGHT_T: nt[j] = 'T'; break; } oligo2 >>= 2; j--; } for (i = 0; i < index1part; i++) { lowbits = oligo1 & LOW_TWO_BITS; switch (lowbits) { case RIGHT_A: nt[j] = 'A'; break; case RIGHT_C: nt[j] = 'C'; break; case RIGHT_G: nt[j] = 'G'; break; case RIGHT_T: nt[j] = 'T'; break; } oligo1 >>= 2; j--; } return nt; } #endif #if 0 struct Cell_T { int querypos; Oligospace_T oligo; }; #endif #if 0 /* Taken from oligo_hr.c */ static int Cell_compare (const void *a, const void *b) { struct Cell_T x = * (struct Cell_T *) a; struct Cell_T y = * (struct Cell_T *) b; if (x.oligo < y.oligo) { return -1; } else if (y.oligo < x.oligo) { return +1; } else { return 0; } } #endif #define BINARY_FOLDDIFF 16 static int binary_search (int lowi, int highi, Oligospace_T *oligos, Oligospace_T goal) { bool foundp = false; int middlei; debug2(printf("entered binary search with lowi=%d, highi=%d, goal=%u\n",lowi,highi,goal)); while (!foundp && lowi < highi) { middlei = lowi + ((highi - lowi) / 2); debug2(printf(" binary: %d:%u %d:%u %d:%u vs. %u\n", lowi,oligos[lowi],middlei,oligos[middlei], highi,oligos[highi],goal)); if (goal < oligos[middlei]) { highi = middlei; } else if (goal > oligos[middlei]) { lowi = middlei + 1; } else { foundp = true; } } if (foundp == true) { debug2(printf("binary search returns %d\n",middlei)); return middlei; } else { debug2(printf("binary search returns %d\n",highi)); return highi; } } #if 0 bool Oligo_mark_repetitive (bool **repetitivep, Oligospace_T *oligos, int first_querypos, int last_querypos) { bool any_repetitive_p = false; struct Cell_T *cells; int n, i, j, querypos, nremaining, binary_threshold; Oligospace_T *q; n = last_querypos - first_querypos + 1; cells = (struct Cell_T *) MALLOCA(n * sizeof(struct Cell_T)); for (i = 0, querypos = first_querypos; i < n; i++, querypos++) { cells[i].querypos = querypos; cells[i].oligo = oligos[querypos]; } qsort(cells,n,sizeof(struct Cell_T),Cell_compare); q = &(repetitive_oligos[0]); nremaining = NREPETITIVE; binary_threshold = BINARY_FOLDDIFF * n; for (i = 0; i < n; i++) { debug2(printf("Testing if %u is repetitive\n",cells[i].oligo)); if (nremaining < binary_threshold) { while (*q < cells[i].oligo) { q++; nremaining--; } debug2(printf(" advanced to oligo %u\n",*q)); } else if (*q < cells[i].oligo) { j = binary_search(1,nremaining,q,cells[i].oligo); q += j; nremaining -= j; } if (*q == cells[i].oligo) { debug2(printf(" Yes it is (position %d)\n",cells[i].querypos)); (*repetitivep)[cells[i].querypos] = true; any_repetitive_p = true; } binary_threshold -= BINARY_FOLDDIFF; } FREEA(cells); return any_repetitive_p; } #endif bool Oligo_repetitive_p (Oligospace_T oligo) { int j; j = binary_search(0,NREPETITIVE,repetitive_oligos,oligo); if (repetitive_oligos[j] == oligo) { return true; } else { return false; } } #if 0 bool Oligo_mark_frequent (bool **frequentp, Oligospace_T *oligos, int n, Oligospace_T *frequent_oligos, int nfrequent) { bool any_frequent_p = false; struct Cell_T *cells; int i, j, nremaining, binary_threshold; Oligospace_T *q; cells = (struct Cell_T *) MALLOCA(n * sizeof(struct Cell_T)); for (i = 0; i < n; i++) { cells[i].querypos = i; cells[i].oligo = oligos[i]; } qsort(cells,n,sizeof(struct Cell_T),Cell_compare); q = &(frequent_oligos[0]); nremaining = nfrequent; binary_threshold = BINARY_FOLDDIFF * n; for (i = 0; i < n; i++) { debug2(printf("Testing if %u is frequent\n",cells[i].oligo)); if (nremaining < binary_threshold) { while (*q < cells[i].oligo) { q++; nremaining--; } debug2(printf(" advanced to oligo %u\n",*q)); } else if (*q < cells[i].oligo) { j = binary_search(1,nremaining,q,cells[i].oligo); q += j; nremaining -= j; } if (*q == cells[i].oligo) { debug2(printf(" Yes it is (position %d)\n",cells[i].querypos)); (*frequentp)[cells[i].querypos] = true; any_frequent_p = true; } binary_threshold -= BINARY_FOLDDIFF; } FREEA(cells); return any_frequent_p; } Oligospace_T * Oligo_frequent_oligos (int *nfrequent, Indexdb_T indexdb, int size_threshold) { Oligospace_T *frequent_oligos, oligo; int npositions, i, k; bool *frequentp[NREPETITIVE]; *nfrequent = 0; memset(frequentp,/*false*/0,NREPETITIVE * sizeof(bool)); for (i = 0; i < NREPETITIVE; i++) { oligo = all_repetitive_oligos[i]; npositions = Indexdb_count_no_subst(indexdb,oligo); if (npositions > size_threshold) { frequentp[i] = true; (*nfrequent) += 1; } } /* Include poly-A and poly-T */ if (frequentp[0] == false) { frequentp[0] = true; (*nfrequent) += 1; } if (frequentp[NREPETITIVE-1] == false) { frequentp[NREPETITIVE-1] = true; (*nfrequent) += 1; } frequent_oligos = (Oligospace_T *) CALLOC(*nfrequent,sizeof(Oligospace_T)); k = 0; for (i = 0; i < NREPETITIVE; i++) { if (frequentp[i] == true) { frequent_oligos[k++] = all_repetitive_oligos[i]; } } return frequent_oligos; } #endif