ABI
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# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.pl'
#########################
# change 'tests => 1' to 'tests => last_test_to_print'
#use FindBin;
#use lib "$FindBin::Bin/..";
use Test::More qw(no_plan);
#BEGIN { plan tests => 1 };
require_ok("ABI");
my $abi = ABI->new("t/TEST_modified.ab1");
isa_ok( $abi, "ABI" );
my @base_calls = $abi->get_base_calls;
#print STDERR "@base_calls";
my @b_calls =
qw(20 33 46 56 67 82 89 102 111 124 136 151 163 174 185 192 204 215
225 233 246 258 274 285 297 308 324 340 349 356 369 383 393 403 413
422 434 447 458 467 477 487 499 513 523 529 544 552 562 570 581 593
603 615 624 634 644 657 668 680 690 702 714 726 736 746 756 766 776
784 796 808 820 830 842 854 863 874 884 897 906 918 930 940 949 960
972 983 996 1005 1017 1027 1039 1049 1063 1074 1086 1097 1109 1117 1131
1143 1153 1163 1174 1186 1196 1208 1218 1232 1243 1255 1266 1278 1288
1298 1310 1323 1333 1345 1357 1368 1380 1392 1402 1413 1425 1436 1448
1459 1469 1481 1493 1504 1513 1524 1537 1547 1559 1570 1583 1595 1606
1616 1629 1638 1650 1664 1673 1684 1694 1704 1716 1727 1737 1749 1761
1774 1786 1796 1810 1820 1834 1844 1855 1865 1874 1887 1900 1913 1926
1937 1946 1958 1970 1983 1994 2007 2019 2029 2040 2055 2066 2075 2088
2102 2112 2121 2134 2146 2159 2169 2180 2192 2206 2218 2230 2239 2254
2264 2276 2286 2302 2314 2323 2338 2350 2360 2371 2382 2395 2408 2418
2432 2442 2454 2467 2479 2489 2502 2516 2528 2540 2551 2565 2574 2587
2598 2610 2621 2634 2644 2656 2667 2682 2693 2705 2716 2727 2740 2753
2766 2778 2790 2803 2816 2827 2838 2852 2865 2876 2887 2898 2912 2924
2934 2945 2957 2969 2982 2992 3005 3016 3028 3040 3053 3065 3075 3091
3103 3115 3128 3138 3151 3164 3176 3189 3201 3214 3226 3237 3251 3262
3276 3285 3299 3313 3322 3337 3350 3360 3373 3385 3398 3410 3423 3435
3445 3460 3472 3484 3496 3509 3520 3531 3544 3557 3569 3581 3593 3604
3615 3628 3640 3653 3664 3674 3687 3700 3714 3725 3739 3751 3763 3773
3787 3797 3810 3821 3834 3847 3859 3871 3883 3897 3909 3921 3935 3946
3959 3970 3982 3994 4007 4019 4031 4044 4057 4069 4078 4091 4101 4116
4127 4142 4154 4166 4176 4190 4202 4215 4227 4240 4252 4265 4277 4288
4301 4313 4326 4337 4351 4362 4373 4385 4397 4410 4422 4436 4448 4459
4471 4484 4497 4508 4523 4535 4545 4558 4569 4582 4596 4608 4621 4633
4645 4656 4670 4681 4695 4708 4719 4733 4744 4755 4768 4781 4794 4806
4819 4830 4842 4856 4867 4880 4891 4902 4915 4928 4941 4954 4966 4979
4991 5002 5016 5027 5039 5052 5065 5077 5089 5103 5115 5128 5139 5153
5166 5177 5190 5203 5214 5225 5238 5251 5262 5274 5285 5298 5310 5323
5336 5348 5360 5372 5386 5399 5412 5423 5437 5450 5462 5473 5488 5499
5510 5523 5535 5547 5558 5570 5584 5596 5609 5622 5635 5646 5658 5670
5681 5692 5706 5718 5732 5744 5756 5770 5782 5797 5810 5822 5835 5847
5860 5872 5884 5897 5908 5921 5934 5948 5959 5971 5983 5996 6008 6020
6033 6046 6059 6072 6085 6096 6110 6123 6134 6149 6161 6172 6187 6200
6210 6224 6235 6248 6259 6272 6285 6299 6312 6324 6339 6352 6364 6375
6389 6402 6414 6426 6439 6451 6463 6477 6489 6502 6513 6528 6541 6554
6568 6580 6593 6603 6617 6632 6644 6658 6671 6682 6695 6709 6721 6734
6747 6758 6770 6783 6795 6807 6820 6833 6845 6858 6871 6884 6895 6908
6920 6934 6947 6960 6972 6985 6996 7011 7024 7038 7051 7063 7077 7088
7100 7115 7127 7140 7151 7162 7176 7191 7203 7220 7230 7241 7254 7267
7279 7294 7307 7322 7335 7347 7361 7371 7383 7395 7410 7423 7434 7450
7461 7473 7487 7499 7510 7520 7533 7548 7559 7570 7583 7597 7610 7622
7637 7653 7663 7673 7684 7699 7711 7723 7735 7747 7761 7774 7789 7801
7813 7828 7838 7851 7864 7876 7888 7901 7917 7930 7941 7954 7967 7980
7995 8008 8020 8032 8043 8054 8065 8074 8086 8099 8112 8126 8140 8153
8164 8177 8188 8202 8211 8221 8230 8239 8249 8262 8274 8287 8301 8315
8326 8342 8354 8366 8378 8391 8406 8419 8431 8443 8456 8471 8481 8490
8499 8508 8519 8530 8541 8552 8566 8579 8592 8604 8616 8629 8642 8655
8668 8680 8693 8708 8723 8734 8745 8756 8769 8780 8792 8804 8814 8829
8842 8851);
is_deeply( \@b_calls, \@base_calls );
is( 1600, $abi->get_max_trace );
is( "M3", $abi->get_sample_name );
my $seq = "TTTTGACGCNCCTTACGCAAATCTCGNCACGAACCTTCCCCTGAAGAAATTGCCAATCTGC
TCGAAAAACCCGTCGCAGAGGTCAAGCGCATGCTTGGACTGAATGAGCGGGTGTCCTCGGTG
GATGTTTCTTTAGGCCCTGATTCCGATAAAACCCTGCTCGATACCCTGACAGATGATCGACCT
ACAGATCCTTGCTAGCTGCTTCAGGACGATGACCTGTCGCAAAGTATCGATCAGTGGTTGTCT
GAACTTACAGACAAGCAGCGTGAGGTGGTGATTCGCCGCTTCGGGTTGCGTGGTCATGAAAGC
AGTACCCTCGAAGATGTTGGTCTGGAGATTGGTCTGACACGCGAACGTGTTCGGCAGATTCAA
GTCGAGGGGCTCAAGCGTTTGCGCGAGATCCTTGAGCGCAACGGTTTGTCCAGTGAGTCGCTG
TTTCAGTAACAGGCATCCTGCTCGCTAAAAAGCCCCGAAATATTCGGGGCTTTTTTGTGCCCG
CAGAATCTGGACCGCTGCTGCCAAGGGGTTTTTTTGAGTGCGTGCGGGTGACCGGTCAGTCTC
AAAAGTGCAGTCAGGCAGGGGTTGGAACTTTATCTGTCATGGGCTGTAAGCCTTTGCTTACCT
TTNATGTAAGCCAAGGGCGAAAACAGGCTTGCGGATAGNTTCGCTTCTGACTTTTCATAGGTT
GNAACTGATTGAAATTTAAACATTNTNATTGTTNTGNTAAGAN";
$seq =~ s/\n//g;
$seq =~ s/\s//g;
is( $seq, $abi->get_sequence() );
#print STDERR $abi->get_sequence_length();
is( 733, $abi->get_sequence_length() );
my @trace = qw(0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 1 3 6 8 11 12 10 7 4 1 0 12 42 92 161 251 341 416 460 462 423
349 254 163 90 38 8 0 0 0 0 0 0 0 0 1 4 8 13 20 26 34 44 56 72 90 110 128
146 163 183 207 242 287 342 405 475 548 622 698 775 852 929 1008 1093 1187
1294 1417 1556 1600 1600 1600 1600 1600 1600 1600 1600 1600 1565 1395 1265
1174 1101 1020 914 775 611 439 281 159 75 25 2 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 13 73 182 339 533 739 898 976 956 843 663 455 276 138 48
4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 23 101 236 420 642 857
1007 1063 1022 913 784 681 633 641 678 706 694 625 507 368 248 183 197
295 458 647 817 928 956 905 800 683 597 570 609 695 793 863 877 821 704
548 381 235 127 54 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 1 4 6 8 10 9 7 4 2 0 0 0 0 0 0 0 0 0 0 0 0 5 59 163 314 495 691
835 892 850 720 533 346 191 80 17 0 0 0 0 0 0 0 0 0 0 0 0 53 165 337 554
803 1005 1112 1099 969 754 509 301 141 42 0 0 5 10 15 20 26 28 30 33 36
41 46 51 54 53 46 35 29 46 110 243 454 729 1028 1292 1461 1491 1380 1165
915 711 618 662 824 1048 1257 1383 1383 1251 1018 735 465 253 109 29 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2
51 147 285 448 623 743 783 743 650 552 500 522 618 755 880 940 906
776 579 379 209 86 17 0 0 0 0 0 0 0 57 204 438 732 1063 1342 1490
1489 1375 1218 1102 1081 1158 1283 1377 1368 1230 992 730 537 480
578 792 1040 1232 1299 1214 998 705 439 222 77 3 0 0 0 0 0 0 0 0 0
0 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 32 127 282 483 709 902 997 967 826 629 452 372 439 652 958
1272 1499 1570 1462 1201 854 534 275 99 10 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 37 135 289 484 699 872 947 906 773 602 467 428
512 696 919 1100 1172 1108 934 718 545 485 562 748 971 1145 1205
1130 955 752 604 569 656 824 998 1099 1080 943 745 563 478 531
713 965 1201 1339 1329 1171 903 605 349 157 42 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 73 182 333 510 688 805 833
768 626 443 275 141 51 6 0 0 0 0 0 0 0 0 1 57 173 349 571
823 1024 1126 1102 961 737 491 283 128 35 0 5 10 12 11 12
9 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 36 159 370 652 978 1282 1460 1466 1299 1011 690 432 314 361
548 806 1045 1190 1195 1060 824 555 325 150 42 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 43 139 284 463 663 817 884 847 715 523 336 180 70 10 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 2 2 1 1 0 0 0 0 0
0 0 0 0 0 0 0 0 34 135 304 528 789 1030 1177 1196 1084 868 601 367
182 61 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
39 145 315 531 773 976 1072 1037 885 670 465 341 344 476 693 924
1095 1150 1070 877 621 386 196 69 6 1 6 9 10 10 10 6 2 0 0 0 0 0
0 0 0 0 0 66 217 450 743 1077 1351 1494 1472 1294 1005 677 399 188
57 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 4 5 6 5 4 2 1 0 0 0 1 2 3 3
2 1 0 0 0 0 0 2 3 4 5 5 4 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 3 7
10 13 15 13 10 6 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 1 1 1 1 0 0 0 0 0 0 1 2 3 3 3 2 1 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 1 4 8 13 17 19 17 13 9 4 2 3 6 10 15 19 20 19 14 9 5 2 0 0 0
0 0 0 0 0 12 77 196 364 566 775 923 975 919 771 567 365 199 83 19 0
1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 1 2 4 7 10 14 18 22 24 25 24 20 15 10 6 2 0 0 1 8 21 42 74 116 166 220 272 316 345 357 348 322 281 231 178 128 85 52 29 16 12 13 21 36 61 97 143 198 256 311 356 383 390 378 350 313 274 239 214
200 197 203 215 228 237 241 236 222 199 171 139 107 76 48 27 13 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 4 4 5 5 5 4 5 5 5 4 4 2 1 0 0 0
2 3 5 6 7 5 4 2 1 0 0 0 1 3 4 6 6 6 5 3 1 1 0 0 0 0 0 0 6 23 52 96 156 225 297 364 417 452 464 453 422 378 329 283 248 226 218 219 226 231 231 224 208 189 171 157 151 154 166 184
203 219 229 231 222 207 187 168 154 148 151 162 177 194 208 215 213 205 191 175 161 154 155 164 179 196 210 218 217 207 192 175 162 156 160 172 190 209 226 236 238 230 212 185 155 123 95 72 54 43 34 26 20 17 16 20 30 44 63 86
113 140 164 183 192 191 180 160 134 107 82 60 45 36 31 30 32 33 32 28 22 15 8 3 0 0 0 2 5 7 9 9 8 5 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 2 3 6 10 16 20 24 26 25 20 14 9 4 1 0 0 1 2 4 5 6 5 4 2 1 0 2 7 13 20 28 36 41 46 49 52 52 49 42 33 23 13 6 2 0 0 0 1 4 9 14 20 25 29
32 32 31 30 28 25 23 20 19 19 23 32 48 73 107 148 195 242 284 317 336 338 323 293 255 212 171 132 101 76 55 38 24 14 7 2 0 4 18 41 74 117 166 212 252 283 300 303 292 270 237 199 160 124 93 70 54 44 37 33
27 21 15 10 7 8 11 16 22 26 29 30 29 26 22 18 13 9 5 2 0 0 0 0 1 4 8 15 22 28 31 31 28 21 14 8 4 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 1 5 10 17 23 27 27 23 17 10 5 1 0 0 0 0 0 3 13 30 57 94 141 193 246 294 332 355 360 348 320 280 233 184 138 97 64 41 27 20 18 18 20 21 22 23 22 20 17 12 8 4 1 0 0 0 8 25
54 93 143 198 252 299 335 358 366 359 340 309 270 227 184 143 107 79 57 42 31 22 14 9 4 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 3 7 10 13
14 11 8 5 2 0 0 0 0 0 2 6 11 17 23 28 32 34 35 34 32 30 26 22 17 14 11 9 10 13 17 21 23 23 18 13 8 3 0 3 7 10 13 14 12 10 7 4 4 4 5 5 4 3 1 0 0 0 0 1
5 11 18 27 37 50 66 86 110 135 159 177 187 187 180 169 157 149 147 152 162 174 186 194 197 196 192 186 178 170 161 153 146 142 141 145 151 159 165 168 166 161 152 142 134 130 131 136 145 157 168 176 181 180 175 169 162 157 156 160
165 173 181 188 191 190 185 176 165 154 147 145 148 155 163 168 168 164 156 145 135 128 126 130 140 155 171 185 195 198 191 178 157 132 105 80 58 41 30 22 19 17 17 16 15 13 11 8 5 2 1 0 0 0 0 0 0 0 0 0
1 2 4 6 9 12 14 16 18 19 23 30 44 65 93 125 158 187 210 223 228 220 204 180 151 119 89 62 41 26 18 14 14 15 16 14 11 7 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4
12 27 47 75 105 135 162 184 200 208 211 207 197 181 161 137 111 87 65 48 36 28 22 18 14 10 5 3 2 2 2 2 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 4 8 12 15 16
15 11 7 5 4 5 8 11 13 13 12 11 9 8 9 11 15 20 27 37 51 69 92 116 141 164 183 196 203 202 192 174 150 122 92 65 43 28 19 15 15 14 13 10 7 3 1 0 0 0 0 0 0 2 7 15 24 35 43 47
45 39 28 18 9 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 4 4 4 3 2 1 0 0 1 3 5 6 7 5 4 2 1 0 0 1 3 4 5 7 8 11 15 23 33 48 65 86 105 120 129 130
121 106 88 69 53 41 33 29 25 22 18 13 8 4 1 0 0 0 0 1 5 10 14 17 19 16 12 7 4 3 4 7 10 14 17 19 20 20 19 19 19 22 28 38 50 66 83 99 111 119 120 115 105 92 78 63 50 38 28 18
11 6 2 0 0 2 11 27 52 84 122 158 190 213 225 227 218 202 179 152 123 94 68 47 30 19 13 10 8 7 5 3 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 4 8
13 19 23 23 22 18 14 11 9 9 10 12 13 14 14 13 12 11 11 12 14 17 21 24 25 24 19 13 8 3 0 3 10 23 42 67 95 123 148 165 174 173 163 146 127 106 88 72 55 38 25 14 5 0 3 16 37 62 88 109
116 107 83 57 33 14 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 5 9 12 17 22 29 39 53 69 84 97 104 103 95 82 66 49 35 23 14 8 5 2 1 0 0 0
0 0 0 0 0 0 0 0 1 5 11 17 23 25 23 17 11 5 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 1 3 4 5 6 6 6 5 6 6 6 5 4 3 1 0 0 0 0 0 1 3 4 5 6 6 6 5 5 5 6 6 6 5 4 3 1 0 0 0 0 0 1 1 1 1 1 0 1 5 13 25 42 65
90 115 137 155 164 166 162 153 142 130 120 113 109 107 108 111 114 116 116 114 108 100 89 77 63 49 37 27 21 18 18 19 20 17 14 9 5 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 1 3 4 5 6 7 7 6 5 4 3 1 0 0 0 0 0 0 0 0 0 0 0 0 1 7 20 41 68 102 137 169 196 214 224 224 216 201 184 167 152 141 136 135 135 136 134 130 123 115 107 102 100 102 108 116 124 130 135
136 133 127 117 104 88 70 52 34 20 10 4 3 11 27 48 77 111 145 177 203 221 231 232 224 209 190 167 144 120 97 74 53 34 20 9 2 0 0 1 7 18 33 53 74 96 114 130 143 153 160 164 164 161 153 142 128 112 94 75
56 41 27 18 13 11 12 17 23 31 39 47 54 59 61 62 63 63 65 68 70 69 64 55 42 28 16 7 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 11 26 47 72 100 128 151 171 186 197 203 203 195 181 160 134
108 84 64 49 40 33 27 21 14 9 4 1 0 0 1 2 3 3 3 2 1 0 0 0 0 0 0 0 0 0 1 2 4 5 6 5 4 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 4 15 32 56 88 124 160 194
223 243 254 254 244 226 203 178 154 132 115 100 89 77 63 48 33 20 11 8 12 22 35 50 64 77 85 89 89 84 76 64 50 37 24 14 6 2 0 0 0 0 0 0 1 3 5 6 6 6 5 4 4 6 9 13 16 16 16 13
9 5 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 8 18 32 53 75 101 126 148 165 178 184 184 180 174 168 163 157 155 152 150 147 143 137 128 119 109
99 92 87 85 87 92 100 109 118 126 130 132 128 120 108 94 79 64 49 36 24 14 7 2 0 0 0 0 0 0 0 0 0 0 0 0 0 5 18 37 62 93 125 155 180 201 218 230 238 240 237 229 218 205 192 180 169 161 152 143
132 120 107 93 79 67 54 44 33 25 16 11 6 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 19 39 65 100 134 168 195 214 224 226 220 210 196 182 170 160 151 145 138 132
124 117 109 103 99 98 99 103 108 112 114 115 114 113 112 111 111 109 103 93 80 64 46 30 17 8 3 0 0 0 0 0 0 0 0 0 0 0 0 6 19 37 60 91 121 149 175 197 216 229 236 234 226 209 186 160 133 107 84 64
48 36 27 19 15 14 17 26 41 60 83 104 124 139 151 158 162 162 160 153 141 124 102 77 51 31 15 4 0 0 0 0 0 0 0 0 0 0 0 0 0 1 3 5 6 8 8 6 5 3 1 0 0 0 0 0 1 3 4 5
5 4 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 7 12 18 24 28 30 30 27 22 16 11 6 2 0 0 0 0 0 0 0 0 0 0
0 0 0 0 1 2 3 4 3 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
1 4 7 10 13 13 10 7 4 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 11 23 40 63 88 114 140 164 185 201 212 214 210
199 184 166 147 131 119 109 102 97 94 90 84 77 66 53 39 25 14 5 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 1 2 2 2 2 1 0 1 5 15 27 45 65 88 109 129 147 165 180 191 199 202 198 185 165 140 114 89 70 57 51 47 43 38 31 21 13 6 2 0 0 0 0 0 0 0 0 0 0 1 5 12 20
30 39 47 51 53 54 55 55 57 59 62 66 69 71 73 74 72 70 66 63 61 60 62 66 70 74 74 69 59 48 35 26 24 30 44 62 81 95 100 95 78 56 36 18 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 2 7 14 23 34 46 58 71 85 103 121 142 160 177 190 198 199 195 186 172 155 138 121 106 93 84 76 69 63 58 53 48 43 38 34 31 29 28 27 28 29 32 37 43 50 59 68 78 88 98 108 113 116 114 109 99 88 76 63
51 40 31 22 15 10 5 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 9 22 39 62 87 112 136 155 171 183 191 195 195 191 185 177 168 158 146 135 122 111 100 93 90 92 98 106
116 121 123 120 111 100 90 81 74 70 68 64 59 51 40 27 17 9 2 0 0 0 0 0 0 0 0 0 0 0 1 9 21 39 61 86 110 132 153 170 184 194 198 195 185 168 144 118 91 66 47 34 26 24 22 20 16 12 7 3
1 1 3 5 6 6 5 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 3 5 8 13 21 32 46 62 76 88 94 96 92 87 81 77 76 79 85 92 99 103 104 100 93 85 76 69 63 59 55 49 42 32 22
13 6 1 0 1 5 10 17 25 32 39 43 46 47 47 45 42 37 32 26 20 16 14 14 14 14 14 11 8 5 2 0 0 0 0 0 0 1 2 3 4 3 2 1 0 0 0 0 0 0 0 0 0 0 1 4 9 17 29 43
58 74 91 107 120 129 134 134 129 120 107 91 73 56 40 27 17 11 8 5 3 2 1 0 0 0 0 0 0 0 0 0 0 0 3 11 23 38 58 79 99 115 128 136 140 138 132 125 117 109 104 100 98 97 96 94 92 87 82 74
65 54 42 30 19 10 4 2 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 7 17 31 50 70 90 107 120 130 137 143 145 146 146 143 137 131 123 115 106 98 92 86
82 79 75 71 66 60 55 51 50 50 52 54 56 55 52 47 40 32 24 16 9 4 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 2 2 1 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 9 19 33 51 70 88 105 119 129 135 137 137 134 130 125 120 115 111 108 104 101 97 94 91 88 86 83 80 76 71 65 58 51 44 38 34 30 29 29 32 36 40 45 50 56
60 64 66 65 62 57 50 41 34 27 23 22 24 28 31 34 36 36 36 35 35 35 36 36 36 34 29 24 19 17 18 25 38 54 73 91 108 121 131 137 140 139 136 131 124 116 109 104 100 99 101 103 105 106 103 98 90 79 65 50
34 21 10 3 0 0 0 4 9 15 21 26 29 27 24 21 18 18 21 27 34 43 49 54 55 56 55 56 57 59 62 63 64 65 65 65 65 65 63 62 59 56 52 48 42 36 29 22 18 16 17 23 33 44 56 66 71 73 71 65
57 46 35 24 14 7 2 0 0 0 0 1 4 7 11 14 16 15 13 12 13 14 19 26 34 43 53 64 74 82 90 94 96 95 92 85 76 65 54 43 35 28 25 22 19 17 13 10 6 3 1 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 4 10 19 28 37 43 45 40 30 22 12 4 5 22 35
);
is_deeply(\@trace,\@array);
is (8853, $abi->get_trace_length());
#print STDERR $abi->get_trace_length();
#my $abi1 = ABI->new("t/TEST_modified.abi");
is(734, $abi->get_corrected_sequence_length());
@base_calls = $abi->get_corrected_base_calls();
@b_calls =
qw(20 33 46 52 56 67 82 89 102 111 124 136 151 163 174 185 192 204 215
225 233 246 258 274 285 297 308 324 340 349 356 369 383 393 403 413
422 434 447 458 467 477 487 499 513 523 529 544 552 562 570 581 593
603 615 624 634 644 657 668 680 690 702 714 726 736 746 756 766 776
784 796 808 820 830 842 854 863 874 884 897 906 918 930 940 949 960
972 983 996 1005 1017 1027 1039 1049 1063 1074 1086 1097 1109 1117 1131
1143 1153 1163 1174 1186 1196 1208 1218 1232 1243 1255 1266 1278 1288
1298 1310 1323 1333 1345 1357 1368 1380 1392 1402 1413 1425 1436 1448
1459 1469 1481 1493 1504 1513 1524 1537 1547 1559 1570 1583 1595 1606
1616 1629 1638 1650 1664 1673 1684 1694 1704 1716 1727 1737 1749 1761
1774 1786 1796 1810 1820 1834 1844 1855 1865 1874 1887 1900 1913 1926
1937 1946 1958 1970 1983 1994 2007 2019 2029 2040 2055 2066 2075 2088
2102 2112 2121 2134 2146 2159 2169 2180 2192 2206 2218 2230 2239 2254
2264 2276 2286 2302 2314 2323 2338 2350 2360 2371 2382 2395 2408 2418
2432 2442 2454 2467 2479 2489 2502 2516 2528 2540 2551 2565 2574 2587
2598 2610 2621 2634 2644 2656 2667 2682 2693 2705 2716 2727 2740 2753
2766 2778 2790 2803 2816 2827 2838 2852 2865 2876 2887 2898 2912 2924
2934 2945 2957 2969 2982 2992 3005 3016 3028 3040 3053 3065 3075 3091
3103 3115 3128 3138 3151 3164 3176 3189 3201 3214 3226 3237 3251 3262
3276 3285 3299 3313 3322 3337 3350 3360 3373 3385 3398 3410 3423 3435
3445 3460 3472 3484 3496 3509 3520 3531 3544 3557 3569 3581 3593 3604
3615 3628 3640 3653 3664 3674 3687 3700 3714 3725 3739 3751 3763 3773
3787 3797 3810 3821 3834 3847 3859 3871 3883 3897 3909 3921 3935 3946
3959 3970 3982 3994 4007 4019 4031 4044 4057 4069 4078 4091 4101 4116
4127 4142 4154 4166 4176 4190 4202 4215 4227 4240 4252 4265 4277 4288
4301 4313 4326 4337 4351 4362 4373 4385 4397 4410 4422 4436 4448 4459
4471 4484 4497 4508 4523 4535 4545 4558 4569 4582 4596 4608 4621 4633
4645 4656 4670 4681 4695 4708 4719 4733 4744 4755 4768 4781 4794 4806
4819 4830 4842 4856 4867 4880 4891 4902 4915 4928 4941 4954 4966 4979
4991 5002 5016 5027 5039 5052 5065 5077 5089 5103 5115 5128 5139 5153
5166 5177 5190 5203 5214 5225 5238 5251 5262 5274 5285 5298 5310 5323
5336 5348 5360 5372 5386 5399 5412 5423 5437 5450 5462 5473 5488 5499
5510 5523 5535 5547 5558 5570 5584 5596 5609 5622 5635 5646 5658 5670
5681 5692 5706 5718 5732 5744 5756 5770 5782 5797 5810 5822 5835 5847
5860 5872 5884 5897 5908 5921 5934 5948 5959 5971 5983 5996 6008 6020
6033 6046 6059 6072 6085 6096 6110 6123 6134 6149 6161 6172 6187 6200
6210 6224 6235 6248 6259 6272 6285 6299 6312 6324 6339 6352 6364 6375
6389 6402 6414 6426 6439 6451 6463 6477 6489 6502 6513 6528 6541 6554
6568 6580 6593 6603 6617 6632 6644 6658 6671 6682 6695 6709 6721 6734
6747 6758 6770 6783 6795 6807 6820 6833 6845 6858 6871 6884 6895 6908
6920 6934 6947 6960 6972 6985 6996 7011 7024 7038 7051 7063 7077 7088
7100 7115 7127 7140 7151 7162 7176 7191 7203 7220 7230 7241 7254 7267
7279 7294 7307 7322 7335 7347 7361 7371 7383 7395 7410 7423 7434 7450
7461 7473 7487 7499 7510 7520 7533 7548 7559 7570 7583 7597 7610 7622
7637 7653 7663 7673 7684 7699 7711 7723 7735 7747 7761 7774 7789 7801
7813 7828 7838 7851 7864 7876 7888 7901 7917 7930 7941 7954 7967 7980
7995 8008 8020 8032 8043 8054 8065 8074 8086 8099 8112 8126 8140 8153
8164 8177 8188 8202 8211 8221 8230 8239 8249 8262 8274 8287 8301 8315
8326 8342 8354 8366 8378 8391 8406 8419 8431 8443 8456 8471 8481 8490
8499 8508 8519 8530 8541 8552 8566 8579 8592 8604 8616 8629 8642 8655
8668 8680 8693 8708 8723 8734 8745 8756 8769 8780 8792 8804 8814 8829
8842 8851);
is_deeply (\@b_calls,\@base_calls);
$seq = "cgcNtGACGCNCCTTACGCAAATCTCGNCACGAACCTTCCCCTGAAGAAATTGCCAATCTGC
TCGAAAAACCCGTCGCAGAGGTCAAGCGCATGCTTGGACTGAATGAGCGGGTGTCCTCGGTG
GATGTTTCTTTAGGCCCTGATTCCGATAAAACCCTGCTCGATACCCTGACAGATGATCGACCT
ACAGATCCTTGCTAGCTGCTTCAGGACGATGACCTGTCGCAAAGTATCGATCAGTGGTTGTCT
GAACTTACAGACAAGCAGCGTGAGGTGGTGATTCGCCGCTTCGGGTTGCGTGGTCATGAAAGC
AGTACCCTCGAAGATGTTGGTCTGGAGATTGGTCTGACACGCGAACGTGTTCGGCAGATTCAA
GTCGAGGGGCTCAAGCGTTTGCGCGAGATCCTTGAGCGCAACGGTTTGTCCAGTGAGTCGCTG
TTTCAGTAACAGGCATCCTGCTCGCTAAAAAGCCCCGAAATATTCGGGGCTTTTTTGTGCCCG
CAGAATCTGGACCGCTGCTGCCAAGGGGTTTTTTTGAGTGCGTGCGGGTGACCGGTCAGTCTC
AAAAGTGCAGTCAGGCAGGGGTTGGAACTTTATCTGTCATGGGCTGTAAGCCTTTGCTTACCT
TTNATGTAAGCCAAGGGCGAAAACAGGCTTGCGGATAGNTTCGCTTCTGACTTTTCATAGGTT
GNAACTGATTGAAATTTAAACATTNTNATTGTTNTGNTAAGAN";
$seq =~ s/\n//g;
$seq =~ s/\s//g;
is ($seq,$abi->get_corrected_sequence);
#print STDERR "\n", $abi->{_index},"\n";
#print STDERR "\n", $abi->{_seq_length_corrected},"\n";
#print "@array", "\n";
#ok(1); # If we made it this far, we're ok.
#########################
# Insert your test code below, the Test module is use()ed here so read
# its man page ( perldoc Test ) for help writing this test script.
( run in 1.391 second using v1.01-cache-2.11-cpan-98e64b0badf )