did some runs

1 month ago · 9f95680620
parent 98e324786c
commit 9f95680620
5 changed files with 3973 additions and 84 deletions
--- a/003.log
+++ b/003.log
@ -0,0 +1,917 @@
 Estimating line count...
 Parsing GFA file...
 Skipped 2418 lines of type: P
 Number of entries: 8347110
 Removing 78 invalid nodes...
 Computing graph stats...
 Computing nodes degrees...
 Computing histogram...
 Stats:
 - Nodes: 3460777
 - Edges: 4886726
 Graph degrees histogram (degree/count):
 - 0: 3
 - 1: 2121
 - 2: 2017208
 - 3: 280128
 - 4: 1047576
 - 5: 69562
 - 6: 20938
 - 7: 8895
 - 8: 4708
 - 9: 2768
 - 10: 1740
 - 11: 1140
 - 12: 873
 - 13: 644
 - 14: 436
 - 15: 339
 - 16: 267
 - 17: 210
 - 18: 183
 - 19: 127
 - 20: 100
 - 21: 97
 - 22: 77
 - 23: 55
 - 24: 48
 - 25: 48
 - 26: 28
 - 27: 33
 - 28: 32
 - 29: 39
 - 30: 29
 - 31: 19
 - 32: 18
 - 33: 17
 - 34: 8
 - 35: 15
 - 36: 7
 - 37: 12
 - 38: 14
 - 39: 10
 - 40: 8
 - 41: 6
 - 42: 8
 - 43: 8
 - 44: 6
 - 45: 10
 - 46: 5
 - 47: 5
 - 48: 6
 - 49: 5
 - 50: 9
 - 51: 2
 - 52: 6
 - 53: 3
 - 54: 4
 - 55: 2
 - 56: 1
 - 57: 8
 - 58: 1
 - 59: 3
 - 60: 3
 - 61: 1
 - 62: 1
 - 63: 5
 - 64: 1
 - 65: 3
 - 66: 1
 - 67: 6
 - 68: 2
 - 69: 1
 - 71: 3
 - 72: 3
 - 73: 2
 - 74: 2
 - 75: 1
 - 78: 1
 - 79: 1
 - 80: 2
 - 81: 1
 - 83: 1
 - 84: 2
 - 85: 2
 - 87: 2
 - 90: 1
 - 91: 1
 - 93: 1
 - 96: 2
 - 97: 3
 - 99: 1
 - 100: 1
 - 101: 2
 - 105: 2
 - 108: 1
 - 110: 1
 - 112: 1
 - 115: 2
 - 116: 1
 - 118: 1
 - 119: 2
 - 126: 1
 - 127: 1
 - 130: 1
 - 131: 1
 - 132: 1
 - 135: 1
 - 136: 1
 - 142: 1
 - 143: 1
 - 150: 1
 - 151: 2
 - 164: 1
 - 165: 1
 - 168: 2
 - 176: 1
 - 183: 1
 - 186: 1
 - 197: 1
 - 206: 1
 - 208: 1
 - 211: 1
 - 229: 1
 - 235: 1
 - 269: 1
 - 310: 1
 - 439: 1
 - 454: 1
 In-degrees histogram (degree/count):
 - 0: 1312
 - 1: 2153708
 - 2: 1239763
 - 3: 49275
 - 4: 9903
 - 5: 2894
 - 6: 1249
 - 7: 663
 - 8: 366
 - 9: 240
 - 10: 199
 - 11: 146
 - 12: 118
 - 13: 92
 - 14: 90
 - 15: 62
 - 16: 59
 - 17: 59
 - 18: 41
 - 19: 39
 - 20: 41
 - 21: 33
 - 22: 29
 - 23: 30
 - 24: 26
 - 25: 24
 - 26: 15
 - 27: 15
 - 28: 14
 - 29: 19
 - 30: 15
 - 31: 12
 - 32: 10
 - 33: 10
 - 34: 7
 - 35: 6
 - 36: 14
 - 37: 9
 - 38: 3
 - 39: 7
 - 40: 7
 - 41: 5
 - 42: 2
 - 43: 9
 - 44: 8
 - 45: 5
 - 46: 4
 - 47: 8
 - 48: 3
 - 50: 2
 - 51: 2
 - 52: 3
 - 53: 4
 - 54: 2
 - 55: 3
 - 56: 3
 - 57: 1
 - 58: 2
 - 59: 1
 - 60: 1
 - 62: 1
 - 63: 3
 - 64: 2
 - 65: 4
 - 66: 4
 - 67: 1
 - 68: 1
 - 69: 1
 - 70: 2
 - 71: 1
 - 72: 1
 - 74: 3
 - 78: 3
 - 79: 1
 - 80: 1
 - 81: 2
 - 83: 2
 - 84: 1
 - 85: 2
 - 88: 1
 - 90: 2
 - 92: 2
 - 94: 1
 - 96: 1
 - 97: 1
 - 100: 3
 - 101: 1
 - 102: 1
 - 104: 1
 - 108: 2
 - 110: 1
 - 111: 1
 - 115: 2
 - 117: 1
 - 118: 1
 - 124: 1
 - 125: 1
 - 129: 1
 - 131: 4
 - 140: 1
 - 147: 1
 - 149: 1
 - 162: 2
 - 163: 1
 - 166: 2
 - 179: 2
 - 184: 1
 - 204: 2
 - 209: 1
 - 226: 1
 - 232: 1
 - 256: 1
 - 302: 1
 - 434: 1
 - 450: 1
 Out-degrees histogram (degree/count):
 - 0: 887
 - 1: 2203729
 - 2: 1169135
 - 3: 54639
 - 4: 15245
 - 5: 6598
 - 6: 3677
 - 7: 2248
 - 8: 1376
 - 9: 897
 - 10: 672
 - 11: 482
 - 12: 320
 - 13: 226
 - 14: 155
 - 15: 119
 - 16: 94
 - 17: 62
 - 18: 48
 - 19: 44
 - 20: 34
 - 21: 23
 - 22: 17
 - 23: 15
 - 24: 1
 - 25: 3
 - 26: 5
 - 27: 9
 - 28: 3
 - 29: 1
 - 30: 5
 - 32: 1
 - 34: 1
 - 35: 1
 - 41: 1
 - 43: 1
 - 44: 2
 - 58: 1
 Computing edge types...
 Computing edge types histogram...
 Node count: 3460774
 Edge count: 4853330, Total edge count: 4853330
 Edge types histogram (type/count):
 - TreeEdge: 3459200
 - ForwardEdge: 352721
 - CrossEdge: 1041409
 Computing connected components...
 Computing sizes histogram...
 Connected components histogram (size/count):
 - 2: 530
 - 3: 1
 - 4: 2
 - 8: 1
 - 92: 1
 - 135: 1
 - 293: 1
 - 305: 1
 - 2286: 1
 - 5040: 1
 - 5639: 1
 - 9714: 1
 - 12885: 1
 - 30694: 1
 - 40082: 1
 - 50661: 1
 - 58952: 1
 - 101785: 1
 - 149492: 1
 - 160217: 1
 - 518117: 1
 - 951450: 1
 - 1361856: 1
 Picking largest connected component...
 Computing graph stats...
 Computing nodes degrees...
 Computing histogram...
 Stats:
 - Nodes: 1361856
 - Edges: 1914711
 Graph degrees histogram (degree/count):
 - 1: 2545
 - 2: 790746
 - 3: 124057
 - 4: 397682
 - 5: 29479
 - 6: 8481
 - 7: 3512
 - 8: 1819
 - 9: 1032
 - 10: 666
 - 11: 448
 - 12: 346
 - 13: 207
 - 14: 167
 - 15: 139
 - 16: 92
 - 17: 81
 - 18: 58
 - 19: 44
 - 20: 35
 - 21: 29
 - 22: 28
 - 23: 24
 - 24: 24
 - 25: 11
 - 26: 4
 - 27: 13
 - 28: 9
 - 29: 13
 - 30: 5
 - 31: 4
 - 32: 2
 - 33: 3
 - 34: 5
 - 35: 2
 - 36: 4
 - 37: 1
 - 38: 1
 - 39: 1
 - 40: 1
 - 41: 1
 - 42: 1
 - 43: 5
 - 44: 4
 - 45: 2
 - 47: 1
 - 50: 1
 - 52: 1
 - 54: 2
 - 57: 1
 - 64: 1
 - 67: 1
 - 72: 1
 - 73: 1
 - 78: 1
 - 83: 1
 - 96: 1
 - 99: 1
 - 100: 1
 - 109: 1
 - 115: 1
 - 119: 1
 - 129: 1
 - 149: 1
 - 163: 1
 - 182: 1
 - 235: 1
 In-degrees histogram (degree/count):
 - 0: 223
 - 1: 859347
 - 2: 472782
 - 3: 21590
 - 4: 4517
 - 5: 1479
 - 6: 669
 - 7: 371
 - 8: 218
 - 9: 126
 - 10: 97
 - 11: 81
 - 12: 52
 - 13: 46
 - 14: 36
 - 15: 24
 - 16: 31
 - 17: 22
 - 18: 10
 - 19: 13
 - 20: 12
 - 21: 16
 - 22: 8
 - 23: 8
 - 24: 7
 - 25: 8
 - 26: 4
 - 27: 3
 - 28: 4
 - 29: 5
 - 30: 2
 - 31: 2
 - 32: 3
 - 33: 1
 - 34: 1
 - 35: 1
 - 36: 3
 - 37: 1
 - 38: 1
 - 39: 1
 - 40: 1
 - 41: 2
 - 43: 5
 - 44: 1
 - 45: 1
 - 48: 1
 - 51: 1
 - 53: 1
 - 56: 1
 - 63: 1
 - 66: 1
 - 70: 1
 - 71: 1
 - 74: 1
 - 83: 1
 - 96: 1
 - 97: 1
 - 100: 1
 - 108: 1
 - 115: 1
 - 118: 1
 - 129: 1
 - 149: 1
 - 162: 1
 - 179: 1
 - 232: 1
 Out-degrees histogram (degree/count):
 - 0: 5593
 - 1: 864226
 - 2: 455228
 - 3: 24556
 - 4: 6340
 - 5: 2439
 - 6: 1296
 - 7: 684
 - 8: 444
 - 9: 289
 - 10: 212
 - 11: 136
 - 12: 101
 - 13: 74
 - 14: 48
 - 15: 41
 - 16: 29
 - 17: 22
 - 18: 24
 - 19: 20
 - 20: 12
 - 21: 7
 - 22: 8
 - 23: 3
 - 25: 3
 - 26: 4
 - 27: 6
 - 29: 3
 - 30: 3
 - 33: 1
 - 41: 1
 - 42: 1
 - 44: 1
 - 52: 1
 Computing edge types...
 Computing edge types histogram...
 Node count: 1361856
 Edge count: 1914711, Total edge count: 1914711
 Edge types histogram (type/count):
 - TreeEdge: 1361619
 - ForwardEdge: 110203
 - CrossEdge: 442889
 Searching for a start node...
 Start node: ("1125070", Reverse)
 NodeDegree { degree: 2, in_degree: 0, out_degree: 2 }
 Orientation histogram:
 - Forward: 1361803
 - Reverse: 53
 Visiting the graph, searching 1 paths...
 Path #1 of length 4146
 Sequence #1 of length 390758
 Searching ACGT in the sequence (naive)...
 Occurrences: [224, 516, 1163, 2921, 3458, 3487, 4201, 4506, 4778, 5847, 5949, 6053, 6266, 6532, 6568, 7026, 7564, 7816, 7935, 7950, 8998, 10867, 12258, 12779, 12970, 14877, 15383, 16423, 20017, 20535, 20802, 22518, 23177, 23947, 24491, 24597, 25118, 26238, 26363, 26926, 26944, 28530, 28798, 30151, 30571, 31459, 32440, 33105, 35476, 35585, 40104, 41617, 42223, 42423, 44627, 44660, 45366, 45588, 47850, 52405, 54283, 56647, 57635, 57942, 58069, 59830, 60076, 63424, 64128, 65087, 65197, 65791, 66269, 66791, 68001, 68581, 68931, 70623, 70907, 71916, 73213, 73445, 75357, 76757, 78201, 79140, 79723, 81794, 82887, 83147, 85157, 87135, 90712, 91304, 91700, 92410, 93060, 93948, 94493, 95003, 96089, 96977, 97917, 99575, 99922, 101150, 101372, 102309, 103486, 104836, 106491, 107057, 107146, 107710, 108252, 108838, 110492, 112248, 112820, 113409, 113490, 115079, 118146, 118560, 119821, 119850, 119920, 120811, 121113, 122957, 126968, 127784, 127793, 129165, 130005, 130068, 130113, 132514, 133552, 133736, 134342, 134751, 135407, 135416, 135697, 137146, 137451, 138032, 138076, 138799, 139051, 139738, 140166, 140255, 140395, 140747, 144270, 145441, 145840, 148891, 148923, 152343, 152993, 153132, 153269, 153963, 154186, 155125, 155666, 155792, 155842, 156284, 156424, 156512, 156889, 157318, 158919, 161299, 161567, 162923, 163849, 164935, 165293, 166627, 169525, 169554, 169663, 170351, 171021, 171031, 171069, 171093, 171129, 171152, 172352, 172744, 172875, 172984, 173013, 173899, 173925, 174007, 174910, 176510, 176939, 177316, 177404, 177544, 177670, 179988, 180211, 181426, 181846, 183021, 186545, 186887, 187027, 187116, 187544, 188233, 188484, 189207, 189251, 189832, 190137, 191586, 191867, 191876, 192532, 192941, 193548, 193732, 196126, 196692, 196742, 196868, 197408, 198344, 198744, 199727, 200792, 201544, 204982, 205431, 206080, 207721, 209377, 212438, 213562, 213584, 214268, 215359, 216165, 216652, 216927, 217153, 218780, 222928, 225043, 225132, 227447, 227644, 227887, 228221, 228511, 229614, 231065, 232180, 234306, 235317, 235648, 240151, 240539, 240913, 242500, 242762, 243210, 244676, 244685, 245082, 246301, 248115, 248412, 248824, 252013, 253657, 254576, 255340, 257458, 258253, 258397, 258509, 263678, 264491, 264754, 264835, 266523, 272073, 274004, 274289, 274843, 275171, 280510, 281552, 281744, 282697, 283688, 284051, 284086, 285696, 285827, 289829, 290921, 292114, 293394, 294480, 295216, 295463, 295541, 296529, 296619, 296666, 296688, 296743, 297452, 298265, 300030, 300165, 300447, 301087, 302337, 303430, 303775, 304979, 305572, 305584, 306559, 306617, 307163, 309846, 311090, 312659, 313326, 313334, 313418, 313746, 315506, 316731, 316959, 317278, 318473, 320032, 321284, 323330, 324048, 324199, 324425, 324583, 324911, 325022, 325096, 325282, 325570, 326300, 327236, 328264, 329039, 329654, 329857, 330470, 330776, 331165, 331417, 331438, 331529, 333140, 334242, 335027, 335104, 337813, 337868, 337890, 337937, 338027, 339093, 339340, 340076, 341162, 342446, 343639, 347506, 348399, 349686, 351314, 351461, 353952, 359726, 362750, 365116, 365154, 366194, 367763, 368244, 368566, 368575, 369179, 369981, 370825, 377002, 378226, 380058, 380657, 381712, 382463, 382844, 384607, 385676, 385877, 385915, 386191, 386429, 386577, 387277]
 Searching ACGT in the sequence (rolling hash)...
 Hash match at position 2205
 => False positive
 Hash match at position 6373
 => False positive
 Hash match at position 12954
 => False positive
 Hash match at position 14196
 => False positive
 Hash match at position 16087
 => False positive
 Hash match at position 16479
 => False positive
 Hash match at position 28799
 => False positive
 Hash match at position 40931
 => False positive
 Hash match at position 45378
 => False positive
 Hash match at position 54233
 => False positive
 Hash match at position 56472
 => False positive
 Hash match at position 62590
 => False positive
 Hash match at position 66523
 => False positive
 Hash match at position 70805
 => False positive
 Hash match at position 72998
 => False positive
 Hash match at position 95694
 => False positive
 Hash match at position 111110
 => False positive
 Hash match at position 113640
 => False positive
 Hash match at position 117003
 => False positive
 Hash match at position 126606
 => False positive
 Hash match at position 134592
 => False positive
 Hash match at position 142190
 => False positive
 Hash match at position 143582
 => False positive
 Hash match at position 144833
 => False positive
 Hash match at position 152670
 => False positive
 Hash match at position 157126
 => False positive
 Hash match at position 183862
 => False positive
 Hash match at position 189224
 => False positive
 Hash match at position 195311
 => False positive
 Hash match at position 195350
 => False positive
 Hash match at position 195972
 => False positive
 Hash match at position 197090
 => False positive
 Hash match at position 213266
 => False positive
 Hash match at position 213618
 => False positive
 Hash match at position 218768
 => False positive
 Hash match at position 225624
 => False positive
 Hash match at position 231613
 => False positive
 Hash match at position 232308
 => False positive
 Hash match at position 245358
 => False positive
 Hash match at position 266712
 => False positive
 Hash match at position 267010
 => False positive
 Hash match at position 272362
 => False positive
 Hash match at position 284700
 => False positive
 Hash match at position 299659
 => False positive
 Hash match at position 308836
 => False positive
 Hash match at position 313218
 => False positive
 Hash match at position 315397
 => False positive
 Hash match at position 324268
 => False positive
 Hash match at position 324848
 => False positive
 Hash match at position 329852
 => False positive
 Hash match at position 330578
 => False positive
 Hash match at position 330906
 => False positive
 Hash match at position 344318
 => False positive
 Hash match at position 346430
 => False positive
 Hash match at position 348288
 => False positive
 Hash match at position 350788
 => False positive
 Hash match at position 354756
 => False positive
 Hash match at position 366826
 => False positive
 Hash match at position 380496
 => False positive
 Hash match at position 387102
 => False positive
 Hash match at position 388787
 => False positive
 Occurrences: []
 Computing k-mer histogram...
 K-mer histogram (kmers/count):
 - AAAA: 1175611
 - AAAC: 592605
 - AAAG: 1009217
 - AAAT: 781229
 - AACA: 428345
 - AACC: 198507
 - AACG: 143889
 - AACT: 577756
 - AAGA: 725774
 - AAGC: 291817
 - AAGG: 439126
 - AAGT: 426031
 - AATA: 584842
 - AATC: 386240
 - AATG: 628293
 - AATT: 413295
 - ACAA: 553292
 - ACAC: 228634
 - ACAG: 374733
 - ACAT: 379962
 - ACCA: 272469
 - ACCC: 152578
 - ACCG: 48967
 - ACCT: 233158
 - ACGA: 117310
 - ACGC: 19760
 - ACGG: 19777
 - ACGT: 103956
 - ACTA: 225547
 - ACTC: 336757
 - ACTG: 323813
 - ACTT: 395383
 - AGAA: 764137
 - AGAC: 208058
 - AGAG: 488851
 - AGAT: 486804
 - AGCA: 282363
 - AGCC: 199259
 - AGCG: 58006
 - AGCT: 285797
 - AGGA: 381807
 - AGGC: 322385
 - AGGG: 218979
 - AGGT: 312993
 - AGTA: 202194
 - AGTC: 191875
 - AGTG: 403423
 - AGTT: 658789
 - ATAA: 384886
 - ATAC: 254291
 - ATAG: 255899
 - ATAT: 638550
 - ATCA: 544681
 - ATCC: 374829
 - ATCG: 51114
 - ATCT: 376117
 - ATGA: 352159
 - ATGC: 407298
 - ATGG: 248757
 - ATGT: 422236
 - ATTA: 328822
 - ATTC: 480158
 - ATTG: 277827
 - ATTT: 616451
 - CAAA: 1160025
 - CAAC: 339887
 - CAAG: 226176
 - CAAT: 347394
 - CACA: 498118
 - CACC: 214464
 - CACG: 45495
 - CACT: 336532
 - CAGA: 547232
 - CAGC: 226023
 - CAGG: 289052
 - CAGT: 352994
 - CATA: 278596
 - CATC: 444599
 - CATG: 270898
 - CATT: 354977
 - CCAA: 506643
 - CCAC: 410796
 - CCAG: 258463
 - CCAT: 357414
 - CCCA: 265718
 - CCCC: 162653
 - CCCG: 129507
 - CCCT: 229539
 - CCGA: 35537
 - CCGC: 33789
 - CCGG: 21445
 - CCGT: 188174
 - CCTA: 151771
 - CCTC: 314128
 - CCTG: 289664
 - CCTT: 355294
 - CGAA: 195019
 - CGAC: 19670
 - CGAG: 57008
 - CGAT: 20153
 - CGCA: 39599
 - CGCC: 26346
 - CGCG: 5115
 - CGCT: 61558
 - CGGA: 32300
 - CGGC: 24269
 - CGGG: 26133
 - CGGT: 37131
 - CGTA: 47617
 - CGTC: 78825
 - CGTG: 67427
 - CGTT: 196299
 - CTAA: 203954
 - CTAC: 297972
 - CTAG: 168160
 - CTAT: 310682
 - CTCA: 388310
 - CTCC: 395302
 - CTCG: 73353
 - CTCT: 522428
 - CTGA: 445358
 - CTGC: 386881
 - CTGG: 268904
 - CTGT: 413674
 - CTTA: 200567
 - CTTC: 459048
 - CTTG: 341872
 - CTTT: 561621
 - GAAA: 725011
 - GAAC: 258832
 - GAAG: 470722
 - GAAT: 590617
 - GACA: 205961
 - GACC: 98841
 - GACG: 31274
 - GACT: 155226
 - GAGA: 436593
 - GAGC: 145298
 - GAGG: 292767
 - GAGT: 402316
 - GATA: 232148
 - GATC: 159086
 - GATG: 199667
 - GATT: 423158
 - GCAA: 294115
 - GCAC: 127547
 - GCAG: 403864
 - GCAT: 198530
 - GCCA: 223527
 - GCCC: 128294
 - GCCG: 20061
 - GCCT: 260304
 - GCGA: 36380
 - GCGC: 41978
 - GCGG: 58791
 - GCGT: 22413
 - GCTA: 181358
 - GCTC: 314922
 - GCTG: 233316
 - GCTT: 351866
 - GGAA: 406305
 - GGAC: 93015
 - GGAG: 249228
 - GGAT: 203915
 - GGCA: 196570
 - GGCC: 199076
 - GGCG: 26020
 - GGCT: 201531
 - GGGA: 256032
 - GGGC: 98165
 - GGGG: 117316
 - GGGT: 172815
 - GGTA: 125848
 - GGTC: 200007
 - GGTG: 199107
 - GGTT: 256618
 - GTAA: 168075
 - GTAC: 96394
 - GTAG: 176689
 - GTAT: 212807
 - GTCA: 195726
 - GTCC: 253476
 - GTCG: 40374
 - GTCT: 221768
 - GTGA: 429479
 - GTGC: 130381
 - GTGG: 228989
 - GTGT: 387431
 - GTTA: 221644
 - GTTC: 365100
 - GTTG: 274241
 - GTTT: 831132
 - TAAA: 491909
 - TAAC: 158133
 - TAAG: 179785
 - TAAT: 296553
 - TACA: 406100
 - TACC: 195575
 - TACG: 40160
 - TACT: 214082
 - TAGA: 241403
 - TAGC: 163290
 - TAGG: 215852
 - TAGT: 275266
 - TATA: 438366
 - TATC: 359197
 - TATG: 332743
 - TATT: 513098
 - TCAA: 720108
 - TCAC: 328384
 - TCAG: 377692
 - TCAT: 414551
 - TCCA: 770252
 - TCCC: 344157
 - TCCG: 79751
 - TCCT: 388066
 - TCGA: 102765
 - TCGC: 37104
 - TCGG: 20005
 - TCGT: 75840
 - TCTA: 422777
 - TCTC: 414391
 - TCTG: 669170
 - TCTT: 460545
 - TGAA: 678939
 - TGAC: 170455
 - TGAG: 481199
 - TGAT: 304456
 - TGCA: 504436
 - TGCC: 208124
 - TGCG: 70442
 - TGCT: 532425
 - TGGA: 282231
 - TGGC: 177301
 - TGGG: 280422
 - TGGT: 257907
 - TGTA: 277680
 - TGTC: 240123
 - TGTG: 503080
 - TGTT: 575702
 - TTAA: 369807
 - TTAC: 207236
 - TTAG: 294207
 - TTAT: 479726
 - TTCA: 714087
 - TTCC: 560032
 - TTCG: 70939
 - TTCT: 849599
 - TTGA: 406602
 - TTGC: 391294
 - TTGG: 250912
 - TTGT: 371033
 - TTTA: 600182
 - TTTC: 890566
 - TTTG: 525339
 - TTTT: 1047325
 Found 256 of 256 possible kmers (about 100.00% coverage)
 Cleaning up...
 cargo run --release -- show -i dataset/chrX.hprc-v1.0-pggb.local.gfa -c 1 -p   230.46s user 32.90s system 98% cpu 4:26.69 total
--- a/004.log
+++ b/004.log
--- a/src/gfa/parser.rs
+++ b/src/gfa/parser.rs
@ -141,16 +141,9 @@ pub fn parse_source<R: Read>(reader: R, line_count: u64) -> io::Result<Vec<Entry
    let mut entries = Vec::new();
    let mut skipped = Vec::new();
-    for line in BufReader::new(reader)
+    println!("Parsing GFA file...");
-        .lines()
+
-        .progress_count(line_count)
+    for line in BufReader::new(reader).lines().progress_count(line_count) {
        .with_style(
            indicatif::ProgressStyle::default_bar()
                .template("{prefix} {spinner} [{elapsed_precise}] [{wide_bar}] {pos}/{len}")
                .unwrap(),
        )
        .with_prefix("parsing source file")
    {
        let line = line?;
        let line = line.trim();
@ -174,6 +167,7 @@ pub fn parse_source<R: Read>(reader: R, line_count: u64) -> io::Result<Vec<Entry
        entries.push(entry);
    }
    // Print skipped lines by compacting same ones together
    for (s, count) in skipped.iter().fold(Vec::new(), |mut acc, s| {
        if let Some((last, count)) = acc.last_mut() {
            if *last == s {
@ -187,11 +181,7 @@ pub fn parse_source<R: Read>(reader: R, line_count: u64) -> io::Result<Vec<Entry
        acc
    }) {
-        if count > 1 {
+        eprintln!("Skipped {} lines of type: {}", count, s);
            eprintln!("skipped {} lines of type: {}", count, s);
        } else {
            eprintln!("skipped line type: {}", s);
        }
    }
    Ok(entries)
--- a/src/main.rs
+++ b/src/main.rs
@ -49,7 +49,7 @@ struct CommandShow {
    #[argh(option, short = 'k', default = "4")]
    /// k-mer length
-    k: usize,
+    kmer_size: usize,
 }
 fn main() -> std::io::Result<()> {
@ -63,25 +63,32 @@ fn main() -> std::io::Result<()> {
                process::exit(1);
            }
            println!("Estimating line count...");
            let file_lines_count = BufReader::new(std::fs::File::open(&opts.input)?)
                .lines()
-                .progress_with(
+                .progress_with(indicatif::ProgressBar::new_spinner())
                    indicatif::ProgressBar::new_spinner().with_message("estimating line count"),
                )
                .count() as u64;
-            let file = std::fs::File::open(opts.input)?;
+            let entries =
-
+                gfa::parser::parse_source(std::fs::File::open(opts.input)?, file_lines_count)?;
            let entries = gfa::parser::parse_source(file, file_lines_count)?;
            println!("Number of entries: {}", entries.len());
            let mut sequence_map = HashMap::new();
            let mut graph: AdjacencyGraph<(String, Orientation)> = AdjacencyGraph::new();
            let mut invalid_nodes = vec![];
            for entry in entries {
                match entry {
                    Entry::Segment { id, sequence } => {
                        // validate sequence is a valid DNA sequence
                        if sequence.chars().any(|c| !"ACGT".contains(c)) {
                            invalid_nodes.push(id.clone());
                            continue;
                        }
                        sequence_map.insert(id.clone(), sequence);
                    }
                    Entry::Link {
@ -96,21 +103,18 @@ fn main() -> std::io::Result<()> {
                }
            }
            println!("Removing {} invalid nodes...", invalid_nodes.len());
            // remove invalid nodes
            for id in invalid_nodes.iter().progress() {
                graph.remove_node(&(id.clone(), Orientation::Forward));
                graph.remove_node(&(id.clone(), Orientation::Reverse));
            }
            println!();
            compute_graph_degrees(&graph);
            let dag = graph.dag();
            // let edge_types = compute_edge_types(&graph);
            // for ((from, to), edge_type) in edge_types.iter() {
            //     match edge_type {
            //         graph::edge_types::EdgeType::BackEdge => {
            //             graph.remove_edge(from, to);
            //         }
            //         _ => {}
            //     }
            // }
            compute_edge_types(&dag.0);
            let ccs = compute_ccs(&dag.0);
@ -151,25 +155,77 @@ fn main() -> std::io::Result<()> {
            for (i, sequence) in sequences.iter().enumerate() {
                println!("Sequence #{} of length {}", i + 1, sequence.len());
-                println!("Searching {} in the sequence (naive)...", opts.pattern);
+                println!("Searching {} (naive)...", opts.pattern);
-                let occurrences = compute_sequence_occurrences_naive(sequence, &opts.pattern);
+                println!(
-                println!("Occurrences: {:?}\n", occurrences);
+                    "Occurrences: {:?}\n",
                    compute_sequence_occurrences_naive(sequence, &opts.pattern)
                );
                println!("Searching {} (rolling hash)...", opts.pattern);
                println!(
-                    "Searching {} in the sequence (rolling hash)...",
+                    "Occurrences: {:?}\n",
-                    opts.pattern
+                    compute_sequence_occurrences_rolling_hash(sequence, &opts.pattern)
                );
                let occurrences =
                    compute_sequence_occurrences_rolling_hash(sequence, &opts.pattern);
                println!("Occurrences: {:?}\n", occurrences);
            }
            compute_kmer_histogram_lb(&sequence_map, &largest_cc_graph, opts.kmer_size);
            println!("Cleaning up...");
            process::exit(0);
        }
    }
 }
 fn compute_kmer_histogram_lb(
    sequence_map: &HashMap<String, String>,
    graph: &DirectedAcyclicGraph<(String, Orientation)>,
    k: usize,
 ) {
    println!("Computing k-mer histogram...");
    let mut kmer_counts = HashMap::new();
    for node in graph.nodes().iter().progress() {
        let sequence = get_node_sequence(sequence_map, &node);
        let kmer_counts_node = sequence_kmer_histogram(&sequence, k);
        for (kmer, count) in kmer_counts_node {
            *kmer_counts.entry(kmer).or_insert(0) += count;
        }
    }
    let mut kmer_counts = kmer_counts.into_iter().collect::<Vec<_>>();
    kmer_counts.sort_by(|a, b| b.1.cmp(&a.1).reverse());
    println!("K-mer histogram (kmers/count):");
    for (kmer, count) in &kmer_counts {
        println!("- {}: {}", kmer, count);
    }
    println!(
        "Found {} of {} possible kmers (about {:.2}% coverage)",
        kmer_counts.len(),
        4usize.pow(k as u32),
        (kmer_counts.len() as f64 / 4usize.pow(k as u32) as f64) * 100.0
    );
 }
 fn sequence_kmer_histogram(sequence: &str, k: usize) -> BTreeMap<String, usize> {
    let mut counts: BTreeMap<String, usize> = BTreeMap::new();
    if sequence.len() < k {
        return counts;
    }
    for i in 0..sequence.len() - k {
        let kmer = &sequence[i..i + k];
        *counts.entry(kmer.to_string()).or_insert(0) += 1;
    }
    counts
 }
 fn letter_to_number(letter: char) -> u64 {
    match letter {
        'A' => 1,
@ -180,6 +236,29 @@ fn letter_to_number(letter: char) -> u64 {
    }
 }
 fn letter_complement(letter: char) -> char {
    match letter {
        'A' => 'T',
        'T' => 'A',
        'C' => 'G',
        'G' => 'C',
        _ => panic!("Invalid letter: {}", letter),
    }
 }
 fn get_node_sequence<'a>(
    sequence_map: &'a HashMap<String, String>,
    node: &(String, Orientation),
 ) -> String {
    let (id, orientation) = node;
    let seq = sequence_map.get(id).expect("sequence not found");
    match orientation {
        Orientation::Forward => seq.clone(),
        Orientation::Reverse => seq.chars().map(letter_complement).rev().collect::<String>(),
    }
 }
 fn compute_sequence_occurrences_rolling_hash(sequence: &str, pattern: &str) -> Vec<usize> {
    let chars = sequence.chars().map(letter_to_number).collect::<Vec<_>>();
@ -191,7 +270,6 @@ fn compute_sequence_occurrences_rolling_hash(sequence: &str, pattern: &str) -> V
    let pattern_hash = rl.hash_pattern(&pattern.chars().map(letter_to_number).collect::<Vec<_>>());
    for i in 0..pattern.len() {
        // println!("Adding letter: {}", chars[i]);
        rl.add_last(chars[i]);
    }
@ -242,23 +320,8 @@ fn compute_sequences(
        let mut sequence = String::new();
        for node in path {
-            let (id, orientation) = node;
+            let piece = get_node_sequence(sequence_map, &node);
-            let seq = sequence_map.get(&id).expect("sequence not found");
+            sequence.push_str(&piece);
            match orientation {
                Orientation::Forward => sequence.push_str(seq),
                Orientation::Reverse => sequence.push_str(
                    &seq.chars()
                        .map(|c| match c {
                            'A' => 'T',
                            'T' => 'A',
                            'C' => 'G',
                            'G' => 'C',
                            _ => panic!("Invalid letter: {}", c),
                        })
                        .rev()
                        .collect::<String>(),
                ),
            }
        }
        sequences.push(sequence);
@ -285,6 +348,7 @@ fn compute_orientation_histogram(graph: &impl Graph<(String, Orientation)>) {
    for (orientation, count) in orientation_histogram.iter() {
        println!("- {:?}: {}", orientation, count);
    }
    println!();
 }
 fn compute_ccs<V>(graph: &AdjacencyGraph<V>) -> Vec<Vec<V>>
@ -307,6 +371,7 @@ where
    for (size, count) in hist.iter() {
        println!("- {}: {}", size, count);
    }
    println!();
    ccs
 }
@ -333,10 +398,12 @@ where
        graph.edges().len(),
        edge_types.len()
    );
    println!("Edge types histogram (type/count):");
    for (edge_type, count) in histogram.iter() {
        println!("- {:?}: {}", edge_type, count);
    }
    println!();
    edge_types
 }
@ -447,35 +514,34 @@ where
    for (degree, count) in histogram.iter() {
        println!("- {}: {}", degree, count);
    }
    println!("In-degrees histogram (degree/count):");
    for (degree, count) in histogram_in.iter() {
        println!("- {}: {}", degree, count);
    }
    println!("Out-degrees histogram (degree/count):");
    for (degree, count) in histogram_out.iter() {
        println!("- {}: {}", degree, count);
    }
    println!();
-    let mut node_degrees = BTreeMap::new();
+    graph
-
+        .nodes()
-    for node in graph.nodes() {
+        .iter()
-        node_degrees.insert(
+        .map(|node| {
            (
                node.clone(),
                NodeDegree {
-                degree: *vertices_degrees.get(&node).expect("node already computed"),
+                    degree: *vertices_degrees.get(node).expect("node already computed"),
                    in_degree: *vertices_in_degrees
-                    .get(&node)
+                        .get(node)
                        .expect("node already computed"),
                    out_degree: *vertices_out_degrees
-                    .get(&node)
+                        .get(node)
                        .expect("node already computed"),
                },
-        );
+            )
-    }
+        })
-
+        .collect()
    node_degrees
 }
 // fn compute_compact_graph<V>(graph: &mut UndirectedGraph<V>) -> UndirectedGraph<V>
--- a/src/rolling_hash/mod.rs
+++ b/src/rolling_hash/mod.rs
@ -66,9 +66,10 @@ where
        };
        // Shift lhs to the right by the difference in offsets
-        let shifted_lhs = (lhs.hash
+        let shifted_lhs = (lhs.hash.wrapping_mul(wrapping_pow_correct(
-            * wrapping_pow_correct(self.alphabet_size, rhs.offset - lhs.offset))
+            self.alphabet_size,
-            % self.modulus;
+            rhs.offset - lhs.offset,
        ))) % self.modulus;
        shifted_lhs == rhs.hash
    }
@ -100,7 +101,11 @@ where
        //     wrapping_pow_correct(self.alphabet_size, i),
        //     self.hash
        // );
-        self.hash += value.into() * wrapping_pow_correct(self.alphabet_size, i);
+        self.hash = self.hash.wrapping_add(
            value
                .into()
                .wrapping_mul(wrapping_pow_correct(self.alphabet_size, i)),
        );
    }
    pub fn remove_first(&mut self) {
@ -108,7 +113,11 @@ where
        let i = self.offset;
-        self.hash -= value.into() * wrapping_pow_correct(self.alphabet_size, i);
+        self.hash = self.hash.wrapping_sub(
            value
                .into()
                .wrapping_mul(wrapping_pow_correct(self.alphabet_size, i)),
        );
        self.offset += 1;
    }