diff --git a/test/data/simulation/unit_data/alignment_sample.txt b/test/data/simulation/unit_data/alignment_sample00.txt similarity index 100% rename from test/data/simulation/unit_data/alignment_sample.txt rename to test/data/simulation/unit_data/alignment_sample00.txt diff --git a/test/data/simulation/unit_data/alignment_sample01.txt b/test/data/simulation/unit_data/alignment_sample01.txt new file mode 100644 index 0000000..d379f8d --- /dev/null +++ b/test/data/simulation/unit_data/alignment_sample01.txt @@ -0,0 +1,510 @@ +SimSeq_ht1_20b4 +1 +250 +9201 +351 +600 +9143 +0 +0 +500 +1 G G 0.000158489 0 0 +2 G F 0.000199526 1 0 +3 T B 0.000501187 2 0 +4 C B 0.000501187 3 0 +5 T = 0.00158489 4 0 +6 C G 0.000158489 5 0 +7 T F 0.000199526 6 0 +8 C B 0.000501187 7 0 +9 T F 0.000199526 8 0 +10 G D 0.000316228 9 0 +11 G G 0.000158489 10 0 +12 T G 0.000158489 11 0 +13 T @ 0.000794328 12 0 +14 A G 0.000158489 13 0 +15 G G 0.000158489 14 0 +16 A F 0.000199526 15 0 +17 C G 0.000158489 16 0 +18 C F 0.000199526 17 0 +19 A G 0.000158489 18 0 +20 G F 0.000199526 19 0 +21 A F 0.000199526 20 0 +22 T G 0.000158489 21 0 +23 C F 0.000199526 22 0 +24 T G 0.000158489 23 0 +25 G G 0.000158489 24 0 +26 A B 0.000501187 25 0 +27 G G 0.000158489 26 0 +28 C F 0.000199526 27 0 +29 C G 0.000158489 28 0 +30 T G 0.000158489 29 0 +31 G D 0.000316228 30 0 +32 G F 0.000199526 31 0 +33 G B 0.000501187 32 0 +34 A G 0.000158489 33 0 +35 G F 0.000199526 34 0 +36 C 3 0.0158489 35 0 +37 T G 0.000158489 36 0 +38 C G 0.000158489 37 0 +39 T G 0.000158489 38 0 +40 C G 0.000158489 39 0 +41 T G 0.000158489 40 0 +42 G G 0.000158489 41 0 +43 G G 0.000158489 42 0 +44 C B 0.000501187 43 0 +45 T G 0.000158489 44 0 +46 A G 0.000158489 45 0 +47 A G 0.000158489 46 0 +48 C G 0.000158489 47 0 +49 T G 0.000158489 48 0 +50 A G 0.000158489 49 0 +51 G G 0.000158489 50 0 +52 G F 0.000199526 51 0 +53 G G 0.000158489 52 0 +54 A G 0.000158489 53 0 +55 A G 0.000158489 54 0 +56 C G 0.000158489 55 0 +57 C G 0.000158489 56 0 +58 C F 0.000199526 57 0 +59 A G 0.000158489 58 0 +60 C G 0.000158489 59 0 +61 T G 0.000158489 60 0 +62 G G 0.000158489 61 0 +63 C F 0.000199526 62 0 +64 T G 0.000158489 63 0 +65 T F 0.000199526 64 0 +66 A G 0.000158489 65 0 +67 A = 0.00158489 66 0 +68 G G 0.000158489 67 0 +69 C 4 0.0125893 68 0 +70 C G 0.000158489 69 0 +71 T @ 0.000794328 70 0 +72 C G 0.000158489 71 0 +73 A G 0.000158489 72 0 +74 A G 0.000158489 73 0 +75 T G 0.000158489 74 0 +76 A G 0.000158489 75 0 +77 A F 0.000199526 76 0 +78 A G 0.000158489 77 0 +79 G F 0.000199526 78 0 +80 C G 0.000158489 79 0 +81 T G 0.000158489 80 0 +82 T G 0.000158489 81 0 +83 G B 0.000501187 82 0 +84 C G 0.000158489 83 0 +85 C G 0.000158489 84 0 +86 T G 0.000158489 85 0 +87 T G 0.000158489 86 0 +88 G G 0.000158489 87 0 +89 A G 0.000158489 88 0 +90 G G 0.000158489 89 0 +91 T G 0.000158489 90 0 +92 G G 0.000158489 91 0 +93 C G 0.000158489 92 0 +94 T G 0.000158489 93 0 +95 T G 0.000158489 94 0 +96 C D 0.000316228 95 0 +97 A G 0.000158489 96 0 +98 A F 0.000199526 97 0 +99 G G 0.000158489 98 0 +100 T G 0.000158489 99 0 +101 A F 0.000199526 100 0 +102 G G 0.000158489 101 0 +103 T 3 0.0158489 102 0 +104 G G 0.000158489 103 0 +105 T G 0.000158489 104 0 +106 G G 0.000158489 105 0 +107 T G 0.000158489 106 0 +108 G G 0.000158489 107 0 +109 C G 0.000158489 108 0 +110 C G 0.000158489 109 0 +111 C G 0.000158489 110 0 +112 G F 0.000199526 111 0 +113 T G 0.000158489 112 0 +114 C G 0.000158489 113 0 +115 T G 0.000158489 114 0 +116 G F 0.000199526 115 0 +117 T G 0.000158489 116 0 +118 T F 0.000199526 117 0 +119 G 1 0.0251189 118 0 +120 T G 0.000158489 119 0 +121 G F 0.000199526 120 0 +122 T G 0.000158489 121 0 +123 G G 0.000158489 122 0 +124 A G 0.000158489 123 0 +125 C G 0.000158489 124 0 +126 T G 0.000158489 125 0 +127 C F 0.000199526 126 0 +128 T F 0.000199526 127 0 +129 G G 0.000158489 128 0 +130 G G 0.000158489 129 0 +131 T G 0.000158489 130 0 +132 A G 0.000158489 131 0 +133 A G 0.000158489 132 0 +134 C G 0.000158489 133 0 +135 T F 0.000199526 134 0 +136 A G 0.000158489 135 0 +137 G F 0.000199526 136 0 +138 A G 0.000158489 137 0 +139 G G 0.000158489 138 0 +140 A G 0.000158489 139 0 +141 T G 0.000158489 140 0 +142 C G 0.000158489 141 0 +143 C G 0.000158489 142 0 +144 C F 0.000199526 143 0 +145 T G 0.000158489 144 0 +146 C G 0.000158489 145 0 +147 A G 0.000158489 146 0 +148 G D 0.000316228 147 0 +149 A G 0.000158489 148 0 +150 C G 0.000158489 149 0 +151 C G 0.000158489 150 0 +152 C G 0.000158489 151 0 +153 T G 0.000158489 152 0 +154 T F 0.000199526 153 0 +155 T G 0.000158489 154 0 +156 T G 0.000158489 155 0 +157 A G 0.000158489 156 0 +158 G G 0.000158489 157 0 +159 T G 0.000158489 158 0 +160 C F 0.000199526 159 0 +161 A G 0.000158489 160 0 +162 G F 0.000199526 161 0 +163 T G 0.000158489 162 0 +164 G G 0.000158489 163 0 +165 T G 0.000158489 164 0 +166 G G 0.000158489 165 0 +167 G G 0.000158489 166 0 +168 A G 0.000158489 167 0 +169 A F 0.000199526 168 0 +170 A G 0.000158489 169 0 +171 A G 0.000158489 170 0 +172 T G 0.000158489 171 0 +173 C G 0.000158489 172 0 +174 T G 0.000158489 173 0 +175 C D 0.000316228 174 0 +176 T G 0.000158489 175 0 +177 A G 0.000158489 176 0 +178 G G 0.000158489 177 0 +179 C F 0.000199526 178 0 +180 A F 0.000199526 179 0 +181 G G 0.000158489 180 0 +182 T F 0.000199526 181 0 +183 G G 0.000158489 182 0 +184 G G 0.000158489 183 0 +185 C F 0.000199526 184 0 +186 G G 0.000158489 185 0 +187 C G 0.000158489 186 0 +188 C G 0.000158489 187 0 +189 C F 0.000199526 188 0 +190 G G 0.000158489 189 0 +191 A D 0.000316228 190 0 +192 A I 0.0001 191 0 +193 C G 0.000158489 192 0 +194 A G 0.000158489 193 0 +195 G G 0.000158489 194 0 +196 G G 0.000158489 195 0 +197 G F 0.000199526 196 0 +198 A G 0.000158489 197 0 +199 C G 0.000158489 198 0 +200 C G 0.000158489 199 0 +201 T F 0.000199526 200 0 +202 G G 0.000158489 201 0 +203 A G 0.000158489 202 0 +204 A G 0.000158489 203 0 +205 A G 0.000158489 204 0 +206 G G 0.000158489 205 0 +207 C G 0.000158489 206 0 +208 G F 0.000199526 207 0 +209 A G 0.000158489 208 0 +210 A G 0.000158489 209 0 +211 A G 0.000158489 210 0 +212 G G 0.000158489 211 0 +213 G G 0.000158489 212 0 +214 G A 0.000630957 213 0 +215 A F 0.000199526 214 0 +216 A . 0.0501187 215 0 +217 A G 0.000158489 216 0 +218 C F 0.000199526 217 0 +219 C G 0.000158489 218 0 +220 A F 0.000199526 219 0 +221 G G 0.000158489 220 0 +222 A G 0.000158489 221 0 +223 G G 0.000158489 222 0 +224 G F 0.000199526 223 0 +225 A F 0.000199526 224 0 +226 G G 0.000158489 225 0 +227 C G 0.000158489 226 0 +228 T G 0.000158489 227 0 +229 C B 0.000501187 228 0 +230 T F 0.000199526 229 0 +231 C F 0.000199526 230 0 +232 T F 0.000199526 231 0 +233 C F 0.000199526 232 0 +234 G F 0.000199526 233 0 +235 A F 0.000199526 234 0 +236 C G 0.000158489 235 0 +237 G F 0.000199526 236 0 +238 C F 0.000199526 237 0 +239 A B 0.000501187 238 0 +240 G D 0.000316228 239 0 +241 G B 0.000501187 240 0 +242 A F 0.000199526 241 0 +243 C B 0.000501187 242 0 +244 T F 0.000199526 243 0 +245 C A 0.000630957 244 0 +246 G G 0.000158489 245 0 +247 G B 0.000501187 246 0 +248 C A 0.000630957 247 0 +249 T F 0.000199526 248 0 +250 T A 0.000630957 249 0 +351 T B 0.000501187 0 1 +352 C F 0.000199526 1 1 +353 A F 0.000199526 2 1 +354 G F 0.000199526 3 1 +355 T 9 0.00398107 4 1 +356 A F 0.000199526 5 1 +357 T F 0.000199526 6 1 +358 T F 0.000199526 7 1 +359 A G 0.000158489 8 1 +360 A F 0.000199526 9 1 +361 G . 0.0501187 10 1 +362 C F 0.000199526 11 1 +363 G D 0.000316228 12 1 +364 G F 0.000199526 13 1 +365 G - 0.0630957 14 1 +366 G F 0.000199526 15 1 +367 G ; 0.00251189 16 1 +368 A F 0.000199526 17 1 +369 G F 0.000199526 18 1 +370 A F 0.000199526 19 1 +371 A F 0.000199526 20 1 +372 T G 0.000158489 21 1 +373 T F 0.000199526 22 1 +374 A G 0.000158489 23 1 +375 G F 0.000199526 24 1 +376 A G 0.000158489 25 1 +377 T G 0.000158489 26 1 +378 C G 0.000158489 27 1 +379 G G 0.000158489 28 1 +380 A G 0.000158489 29 1 +381 T G 0.000158489 30 1 +382 G - 0.0630957 31 1 +383 G G 0.000158489 32 1 +384 G G 0.000158489 33 1 +385 A G 0.000158489 34 1 +386 A G 0.000158489 35 1 +387 A D 0.000316228 36 1 +388 A G 0.000158489 37 1 +389 A F 0.000199526 38 1 +390 A G 0.000158489 39 1 +391 T G 0.000158489 40 1 +392 T G 0.000158489 41 1 +393 C G 0.000158489 42 1 +394 G G 0.000158489 43 1 +395 G G 0.000158489 44 1 +396 T G 0.000158489 45 1 +397 T F 0.000199526 46 1 +398 A F 0.000199526 47 1 +399 A G 0.000158489 48 1 +400 G G 0.000158489 49 1 +401 G G 0.000158489 50 1 +402 C G 0.000158489 51 1 +403 C G 0.000158489 52 1 +404 A G 0.000158489 53 1 +405 G G 0.000158489 54 1 +406 G G 0.000158489 55 1 +407 G F 0.000199526 56 1 +408 G G 0.000158489 57 1 +409 G G 0.000158489 58 1 +410 A F 0.000199526 59 1 +411 A G 0.000158489 60 1 +412 A F 0.000199526 61 1 +413 G G 0.000158489 62 1 +414 A F 0.000199526 63 1 +415 A G 0.000158489 64 1 +416 A G 0.000158489 65 1 +417 A G 0.000158489 66 1 +418 A G 0.000158489 67 1 +419 A G 0.000158489 68 1 +420 T G 0.000158489 69 1 +421 A F 0.000199526 70 1 +422 T G 0.000158489 71 1 +423 A G 0.000158489 72 1 +424 A G 0.000158489 73 1 +425 A G 0.000158489 74 1 +426 T F 0.000199526 75 1 +427 T G 0.000158489 76 1 +428 A G 0.000158489 77 1 +429 A G 0.000158489 78 1 +430 A G 0.000158489 79 1 +431 A F 0.000199526 80 1 +432 C F 0.000199526 81 1 +433 A G 0.000158489 82 1 +434 T G 0.000158489 83 1 +435 A G 0.000158489 84 1 +436 T G 0.000158489 85 1 +437 A G 0.000158489 86 1 +438 G F 0.000199526 87 1 +439 T F 0.000199526 88 1 +440 A G 0.000158489 89 1 +441 T G 0.000158489 90 1 +442 G F 0.000199526 91 1 +443 G G 0.000158489 92 1 +444 G G 0.000158489 93 1 +445 C G 0.000158489 94 1 +446 A G 0.000158489 95 1 +447 A G 0.000158489 96 1 +448 G F 0.000199526 97 1 +449 C G 0.000158489 98 1 +450 A G 0.000158489 99 1 +451 G G 0.000158489 100 1 +452 G F 0.000199526 101 1 +453 G G 0.000158489 102 1 +454 A G 0.000158489 103 1 +455 G G 0.000158489 104 1 +456 C F 0.000199526 105 1 +457 T G 0.000158489 106 1 +458 A F 0.000199526 107 1 +459 G G 0.000158489 108 1 +460 A G 0.000158489 109 1 +461 A G 0.000158489 110 1 +462 C G 0.000158489 111 1 +463 G G 0.000158489 112 1 +464 A G 0.000158489 113 1 +465 T B 0.000501187 114 1 +466 T G 0.000158489 115 1 +467 C G 0.000158489 116 1 +468 G G 0.000158489 117 1 +469 C G 0.000158489 118 1 +470 A F 0.000199526 119 1 +471 G G 0.000158489 120 1 +472 T F 0.000199526 121 1 +473 T G 0.000158489 122 1 +474 A G 0.000158489 123 1 +475 A G 0.000158489 124 1 +476 T G 0.000158489 125 1 +477 C G 0.000158489 126 1 +478 C G 0.000158489 127 1 +479 T F 0.000199526 128 1 +480 G F 0.000199526 129 1 +481 G F 0.000199526 130 1 +482 C G 0.000158489 131 1 +483 C F 0.000199526 132 1 +484 T 1 0.0251189 133 1 +485 G F 0.000199526 134 1 +486 T G 0.000158489 135 1 +487 T G 0.000158489 136 1 +488 A G 0.000158489 137 1 +489 G F 0.000199526 138 1 +490 A G 0.000158489 139 1 +491 A G 0.000158489 140 1 +492 A G 0.000158489 141 1 +493 C G 0.000158489 142 1 +494 A G 0.000158489 143 1 +495 T G 0.000158489 144 1 +496 C G 0.000158489 145 1 +497 A 3 0.0158489 146 1 +498 G G 0.000158489 147 1 +499 A G 0.000158489 148 1 +500 A G 0.000158489 149 1 +501 G F 0.000199526 150 1 +502 G G 0.000158489 151 1 +503 C F 0.000199526 152 1 +504 T G 0.000158489 153 1 +505 G G 0.000158489 154 1 +506 T G 0.000158489 155 1 +507 A G 0.000158489 156 1 +508 G G 0.000158489 157 1 +509 A F 0.000199526 158 1 +510 C G 0.000158489 159 1 +511 A G 0.000158489 160 1 +512 A G 0.000158489 161 1 +513 A G 0.000158489 162 1 +514 T F 0.000199526 163 1 +515 A G 0.000158489 164 1 +516 C G 0.000158489 165 1 +517 T 1 0.0251189 166 1 +518 G F 0.000199526 167 1 +519 G 4 0.0125893 168 1 +520 G G 0.000158489 169 1 +521 A G 0.000158489 170 1 +522 C G 0.000158489 171 1 +523 A G 0.000158489 172 1 +524 G A 0.000630957 173 1 +525 C G 0.000158489 174 1 +526 T G 0.000158489 175 1 +527 A G 0.000158489 176 1 +528 C G 0.000158489 177 1 +529 A G 0.000158489 178 1 +530 A G 0.000158489 179 1 +531 C G 0.000158489 180 1 +532 C F 0.000199526 181 1 +533 A G 0.000158489 182 1 +534 T G 0.000158489 183 1 +535 C F 0.000199526 184 1 +536 C F 0.000199526 185 1 +537 C G 0.000158489 186 1 +538 T G 0.000158489 187 1 +539 T G 0.000158489 188 1 +540 C G 0.000158489 189 1 +541 A G 0.000158489 190 1 +542 G F 0.000199526 191 1 +543 A G 0.000158489 192 1 +544 C G 0.000158489 193 1 +545 A G 0.000158489 194 1 +546 G G 0.000158489 195 1 +547 G G 0.000158489 196 1 +548 A G 0.000158489 197 1 +549 T G 0.000158489 198 1 +550 C G 0.000158489 199 1 +551 A F 0.000199526 200 1 +552 G G 0.000158489 201 1 +553 A G 0.000158489 202 1 +554 A F 0.000199526 203 1 +555 G G 0.000158489 204 1 +556 A G 0.000158489 205 1 +557 A F 0.000199526 206 1 +558 C F 0.000199526 207 1 +559 T G 0.000158489 208 1 +560 T G 0.000158489 209 1 +561 A G 0.000158489 210 1 +562 G F 0.000199526 211 1 +563 A G 0.000158489 212 1 +564 T G 0.000158489 213 1 +565 C F 0.000199526 214 1 +566 A G 0.000158489 215 1 +567 T G 0.000158489 216 1 +568 T F 0.000199526 217 1 +569 A G 0.000158489 218 1 +570 T G 0.000158489 219 1 +571 A G 0.000158489 220 1 +572 T G 0.000158489 221 1 +573 A G 0.000158489 222 1 +574 A G 0.000158489 223 1 +575 T G 0.000158489 224 1 +576 A ; 0.00251189 225 1 +577 C G 0.000158489 226 1 +578 A G 0.000158489 227 1 +579 G G 0.000158489 228 1 +580 T G 0.000158489 229 1 +581 A G 0.000158489 230 1 +582 G F 0.000199526 231 1 +583 C F 0.000199526 232 1 +584 N # 0.630957 233 1 +585 A F 0.000199526 234 1 +586 C F 0.000199526 235 1 +587 C G 0.000158489 236 1 +588 C F 0.000199526 237 1 +589 T F 0.000199526 238 1 +590 C G 0.000158489 239 1 +591 T F 0.000199526 240 1 +592 A G 0.000158489 241 1 +593 T G 0.000158489 242 1 +594 T 0 0.0316228 243 1 +595 G B 0.000501187 244 1 +596 T G 0.000158489 245 1 +597 G G 0.000158489 246 1 +598 T F 0.000199526 247 1 +599 G F 0.000199526 248 1 +600 C A 0.000630957 249 1 diff --git a/test/data/simulation/unit_data/alignment_sample02.txt b/test/data/simulation/unit_data/alignment_sample02.txt new file mode 100644 index 0000000..b9db105 --- /dev/null +++ b/test/data/simulation/unit_data/alignment_sample02.txt @@ -0,0 +1,510 @@ +SimSeq_ht1_1636 +607 +856 +9285 +957 +1206 +9106 +6.24744e-125 +0 +500 +607 G A 0.000630957 0 0 +608 G A 0.000630957 1 0 +609 A G 0.000158489 2 0 +610 T F 0.000199526 3 0 +611 A G 0.000158489 4 0 +612 G F 0.000199526 5 0 +613 A G 0.000158489 6 0 +614 G G 0.000158489 7 0 +615 A F 0.000199526 8 0 +616 T G 0.000158489 9 0 +617 A G 0.000158489 10 0 +618 A F 0.000199526 11 0 +619 A G 0.000158489 12 0 +620 A G 0.000158489 13 0 +621 G F 0.000199526 14 0 +622 A F 0.000199526 15 0 +623 C G 0.000158489 16 0 +624 A F 0.000199526 17 0 +625 C F 0.000199526 18 0 +626 C G 0.000158489 19 0 +627 A G 0.000158489 20 0 +628 A F 0.000199526 21 0 +629 G G 0.000158489 22 0 +630 G G 0.000158489 23 0 +631 A G 0.000158489 24 0 +632 A 0 0.0316228 25 0 +633 G G 0.000158489 26 0 +634 C F 0.000199526 27 0 +635 T ; 0.00251189 28 0 +636 T G 0.000158489 29 0 +637 T G 0.000158489 30 0 +638 A G 0.000158489 31 0 +639 G G 0.000158489 32 0 +640 A G 0.000158489 33 0 +641 C G 0.000158489 34 0 +642 A 9 0.00398107 35 0 +643 A G 0.000158489 36 0 +644 G G 0.000158489 37 0 +645 A G 0.000158489 38 0 +646 T G 0.000158489 39 0 +647 A G 0.000158489 40 0 +648 G G 0.000158489 41 0 +649 A G 0.000158489 42 0 +650 G G 0.000158489 43 0 +651 G G 0.000158489 44 0 +652 A G 0.000158489 45 0 +653 A G 0.000158489 46 0 +654 G G 0.000158489 47 0 +655 A F 0.000199526 48 0 +656 G G 0.000158489 49 0 +657 C G 0.000158489 50 0 +658 A G 0.000158489 51 0 +659 A G 0.000158489 52 0 +660 A F 0.000199526 53 0 +661 A G 0.000158489 54 0 +662 C G 0.000158489 55 0 +663 A G 0.000158489 56 0 +664 A G 0.000158489 57 0 +665 A F 0.000199526 58 0 +666 A G 0.000158489 59 0 +667 G G 0.000158489 60 0 +668 T G 0.000158489 61 0 +669 A A 0.000630957 62 0 +670 A G 0.000158489 63 0 +671 G G 0.000158489 64 0 +672 A G 0.000158489 65 0 +673 A G 0.000158489 66 0 +674 A G 0.000158489 67 0 +675 A G 0.000158489 68 0 +676 A G 0.000158489 69 0 +677 A F 0.000199526 70 0 +678 G G 0.000158489 71 0 +679 C G 0.000158489 72 0 +680 A G 0.000158489 73 0 +681 C G 0.000158489 74 0 +682 A G 0.000158489 75 0 +683 G G 0.000158489 76 0 +684 C G 0.000158489 77 0 +685 A G 0.000158489 78 0 +686 A G 0.000158489 79 0 +687 G G 0.000158489 80 0 +688 C G 0.000158489 81 0 +689 A G 0.000158489 82 0 +690 G G 0.000158489 83 0 +691 C G 0.000158489 84 0 +692 A D 0.000316228 85 0 +693 G F 0.000199526 86 0 +694 C G 0.000158489 87 0 +695 T G 0.000158489 88 0 +696 G G 0.000158489 89 0 +697 A G 0.000158489 90 0 +698 C F 0.000199526 91 0 +699 A G 0.000158489 92 0 +700 C @ 0.000794328 93 0 +701 A G 0.000158489 94 0 +702 G F 0.000199526 95 0 +703 G G 0.000158489 96 0 +704 A G 0.000158489 97 0 +705 C G 0.000158489 98 0 +706 A G 0.000158489 99 0 +707 C G 0.000158489 100 0 +708 A G 0.000158489 101 0 +709 G G 0.000158489 102 0 +710 C G 0.000158489 103 0 +711 A G 0.000158489 104 0 +712 A G 0.000158489 105 0 +713 T G 0.000158489 106 0 +714 C F 0.000199526 107 0 +715 A G 0.000158489 108 0 +716 G G 0.000158489 109 0 +717 G G 0.000158489 110 0 +718 T @ 0.000794328 111 0 +719 C G 0.000158489 112 0 +720 A G 0.000158489 113 0 +721 G G 0.000158489 114 0 +722 C F 0.000199526 115 0 +723 C G 0.000158489 116 0 +724 A G 0.000158489 117 0 +725 A G 0.000158489 118 0 +726 A G 0.000158489 119 0 +727 A G 0.000158489 120 0 +728 T F 0.000199526 121 0 +729 T G 0.000158489 122 0 +730 A G 0.000158489 123 0 +731 C G 0.000158489 124 0 +732 C F 0.000199526 125 0 +733 C F 0.000199526 126 0 +734 T G 0.000158489 127 0 +735 A G 0.000158489 128 0 +736 T G 0.000158489 129 0 +737 A G 0.000158489 130 0 +738 G G 0.000158489 131 0 +739 T G 0.000158489 132 0 +740 G G 0.000158489 133 0 +741 C G 0.000158489 134 0 +742 A G 0.000158489 135 0 +743 G G 0.000158489 136 0 +744 A G 0.000158489 137 0 +745 A G 0.000158489 138 0 +746 C G 0.000158489 139 0 +747 A G 0.000158489 140 0 +748 T G 0.000158489 141 0 +749 C D 0.000316228 142 0 +750 C F 0.000199526 143 0 +751 A G 0.000158489 144 0 +752 G G 0.000158489 145 0 +753 G G 0.000158489 146 0 +754 G G 0.000158489 147 0 +755 G B 0.000501187 148 0 +756 C F 0.000199526 149 0 +757 A G 0.000158489 150 0 +758 A G 0.000158489 151 0 +759 A G 0.000158489 152 0 +760 T G 0.000158489 153 0 +761 G G 0.000158489 154 0 +762 G G 0.000158489 155 0 +763 T G 0.000158489 156 0 +764 A G 0.000158489 157 0 +765 C G 0.000158489 158 0 +766 A G 0.000158489 159 0 +767 T G 0.000158489 160 0 +768 C G 0.000158489 161 0 +769 A G 0.000158489 162 0 +770 G G 0.000158489 163 0 +771 G G 0.000158489 164 0 +772 C G 0.000158489 165 0 +773 C F 0.000199526 166 0 +774 A G 0.000158489 167 0 +775 T G 0.000158489 168 0 +776 A F 0.000199526 169 0 +777 T F 0.000199526 170 0 +778 C G 0.000158489 171 0 +779 A G 0.000158489 172 0 +780 C G 0.000158489 173 0 +781 C G 0.000158489 174 0 +782 T F 0.000199526 175 0 +783 A G 0.000158489 176 0 +784 G G 0.000158489 177 0 +785 A G 0.000158489 178 0 +786 A G 0.000158489 179 0 +787 C G 0.000158489 180 0 +788 T G 0.000158489 181 0 +789 T G 0.000158489 182 0 +790 T F 0.000199526 183 0 +791 A G 0.000158489 184 0 +792 A G 0.000158489 185 0 +793 A G 0.000158489 186 0 +794 T G 0.000158489 187 0 +795 A 0 0.0316228 188 0 +796 C G 0.000158489 189 0 +797 A F 0.000199526 190 0 +798 T G 0.000158489 191 0 +799 G G 0.000158489 192 0 +800 G G 0.000158489 193 0 +801 G G 0.000158489 194 0 +802 T G 0.000158489 195 0 +803 A G 0.000158489 196 0 +804 A G 0.000158489 197 0 +805 A G 0.000158489 198 0 +806 A G 0.000158489 199 0 +807 G G 0.000158489 200 0 +808 T G 0.000158489 201 0 +809 A G 0.000158489 202 0 +810 G G 0.000158489 203 0 +811 T G 0.000158489 204 0 +812 A G 0.000158489 205 0 +813 G G 0.000158489 206 0 +814 A G 0.000158489 207 0 +815 A G 0.000158489 208 0 +816 G F 0.000199526 209 0 +817 A G 0.000158489 210 0 +818 G F 0.000199526 211 0 +819 A G 0.000158489 212 0 +820 A G 0.000158489 213 0 +821 G F 0.000199526 214 0 +822 G A 0.000630957 215 0 +823 C G 0.000158489 216 0 +824 T G 0.000158489 217 0 +825 T G 0.000158489 218 0 +826 T G 0.000158489 219 0 +827 C F 0.000199526 220 0 +828 A F 0.000199526 221 0 +829 G G 0.000158489 222 0 +830 C G 0.000158489 223 0 +831 C G 0.000158489 224 0 +832 C F 0.000199526 225 0 +833 A F 0.000199526 226 0 +834 G F 0.000199526 227 0 +835 A G 0.000158489 228 0 +836 A F 0.000199526 229 0 +837 G F 0.000199526 230 0 +838 T ; 0.00251189 231 0 +839 G F 0.000199526 232 0 +840 A F 0.000199526 233 0 +841 T G 0.000158489 234 0 +842 A F 0.000199526 235 0 +843 C F 0.000199526 236 0 +844 C F 0.000199526 237 0 +845 C F 0.000199526 238 0 +846 A F 0.000199526 239 0 +847 T G 0.000158489 240 0 +848 G F 0.000199526 241 0 +849 T F 0.000199526 242 0 +850 T B 0.000501187 243 0 +851 T F 0.000199526 244 0 +852 T A 0.000630957 245 0 +853 C A 0.000630957 246 0 +854 A B 0.000501187 247 0 +855 G F 0.000199526 248 0 +856 C > 0.00125893 249 0 +957 G B 0.000501187 0 1 +958 A F 0.000199526 1 1 +959 A F 0.000199526 2 1 +960 G F 0.000199526 3 1 +961 C F 0.000199526 4 1 +962 T B 0.000501187 5 1 +963 G . 0.0501187 6 1 +964 C F 0.000199526 7 1 +965 A F 0.000199526 8 1 +966 G . 0.0501187 9 1 +967 A B 0.000501187 10 1 +968 A F 0.000199526 11 1 +969 T F 0.000199526 12 1 +970 G F 0.000199526 13 1 +971 G F 0.000199526 14 1 +972 G F 0.000199526 15 1 +973 A B 0.000501187 16 1 +974 T F 0.000199526 17 1 +975 A F 0.000199526 18 1 +976 G F 0.000199526 19 1 +977 A F 0.000199526 20 1 +978 G F 0.000199526 21 1 +979 T F 0.000199526 22 1 +980 G G 0.000158489 23 1 +981 C F 0.000199526 24 1 +982 A 9 0.00398107 25 1 +983 T G 0.000158489 26 1 +984 C F 0.000199526 27 1 +985 C 0 0.0316228 28 1 +986 A G 0.000158489 29 1 +987 G F 0.000199526 30 1 +988 T G 0.000158489 31 1 +989 G F 0.000199526 32 1 +990 C A 0.000630957 33 1 +991 A G 0.000158489 34 1 +992 T G 0.000158489 35 1 +993 G G 0.000158489 36 1 +994 C G 0.000158489 37 1 +995 A G 0.000158489 38 1 +996 G F 0.000199526 39 1 +997 G F 0.000199526 40 1 +998 G G 0.000158489 41 1 +999 C G 0.000158489 42 1 +1000 C G 0.000158489 43 1 +1001 T G 0.000158489 44 1 +1002 A G 0.000158489 45 1 +1003 T G 0.000158489 46 1 +1004 T G 0.000158489 47 1 +1005 G G 0.000158489 48 1 +1006 C G 0.000158489 49 1 +1007 A G 0.000158489 50 1 +1008 C F 0.000199526 51 1 +1009 C F 0.000199526 52 1 +1010 A G 0.000158489 53 1 +1011 G G 0.000158489 54 1 +1012 G G 0.000158489 55 1 +1013 C G 0.000158489 56 1 +1014 C G 0.000158489 57 1 +1015 A G 0.000158489 58 1 +1016 G F 0.000199526 59 1 +1017 A G 0.000158489 60 1 +1018 T D 0.000316228 61 1 +1019 G B 0.000501187 62 1 +1020 A A 0.000630957 63 1 +1021 G F 0.000199526 64 1 +1022 A G 0.000158489 65 1 +1023 G G 0.000158489 66 1 +1024 A G 0.000158489 67 1 +1025 A G 0.000158489 68 1 +1026 C G 0.000158489 69 1 +1027 C > 0.00125893 70 1 +1028 A G 0.000158489 71 1 +1029 A < 0.00199526 72 1 +1030 G G 0.000158489 73 1 +1031 G F 0.000199526 74 1 +1032 G G 0.000158489 75 1 +1033 G F 0.000199526 76 1 +1034 A G 0.000158489 77 1 +1035 A G 0.000158489 78 1 +1036 G G 0.000158489 79 1 +1037 T G 0.000158489 80 1 +1038 G @ 0.000794328 81 1 +1039 A F 0.000199526 82 1 +1040 C F 0.000199526 83 1 +1041 A G 0.000158489 84 1 +1042 T F 0.000199526 85 1 +1043 A G 0.000158489 86 1 +1044 G G 0.000158489 87 1 +1045 C G 0.000158489 88 1 +1046 A G 0.000158489 89 1 +1047 G G 0.000158489 90 1 +1048 G F 0.000199526 91 1 +1049 A G 0.000158489 92 1 +1050 A G 0.000158489 93 1 +1051 C G 0.000158489 94 1 +1052 T G 0.000158489 95 1 +1053 A ; 0.00251189 96 1 +1054 C G 0.000158489 97 1 +1055 T G 0.000158489 98 1 +1056 A G 0.000158489 99 1 +1057 G G 0.000158489 100 1 +1058 T G 0.000158489 101 1 +1059 A G 0.000158489 102 1 +1060 C F 0.000199526 103 1 +1061 C G 0.000158489 104 1 +1062 C G 0.000158489 105 1 +1063 T G 0.000158489 106 1 +1064 T G 0.000158489 107 1 +1065 C G 0.000158489 108 1 +1066 A G 0.000158489 109 1 +1067 G F 0.000199526 110 1 +1068 G F 0.000199526 111 1 +1069 A G 0.000158489 112 1 +1070 A G 0.000158489 113 1 +1071 C G 0.000158489 114 1 +1072 A F 0.000199526 115 1 +1073 A G 0.000158489 116 1 +1074 A > 0.00125893 117 1 +1075 T G 0.000158489 118 1 +1076 A G 0.000158489 119 1 +1077 G G 0.000158489 120 1 +1078 G D 0.000316228 121 1 +1079 A G 0.000158489 122 1 +1080 T G 0.000158489 123 1 +1081 G F 0.000199526 124 1 +1082 G G 0.000158489 125 1 +1083 A G 0.000158489 126 1 +1084 T G 0.000158489 127 1 +1085 G G 0.000158489 128 1 +1086 A G 0.000158489 129 1 +1087 C G 0.000158489 130 1 +1088 A G 0.000158489 131 1 +1089 A G 0.000158489 132 1 +1090 A G 0.000158489 133 1 +1091 T G 0.000158489 134 1 +1092 A G 0.000158489 135 1 +1093 A D 0.000316228 136 1 +1094 T G 0.000158489 137 1 +1095 C G 0.000158489 138 1 +1096 C G 0.000158489 139 1 +1097 A G 0.000158489 140 1 +1098 C G 0.000158489 141 1 +1099 C G 0.000158489 142 1 +1100 T F 0.000199526 143 1 +1101 A G 0.000158489 144 1 +1102 T G 0.000158489 145 1 +1103 C G 0.000158489 146 1 +1104 C G 0.000158489 147 1 +1105 C G 0.000158489 148 1 +1106 A G 0.000158489 149 1 +1107 G . 0.0501187 150 1 +1108 T G 0.000158489 151 1 +1109 A G 0.000158489 152 1 +1110 G G 0.000158489 153 1 +1111 G G 0.000158489 154 1 +1112 A F 0.000199526 155 1 +1113 G G 0.000158489 156 1 +1114 A G 0.000158489 157 1 +1115 A G 0.000158489 158 1 +1116 A 1 0.0251189 159 1 +1117 T G 0.000158489 160 1 +1118 T G 0.000158489 161 1 +1119 T G 0.000158489 162 1 +1120 A G 0.000158489 163 1 +1121 T G 0.000158489 164 1 +1122 A F 0.000199526 165 1 +1123 A G 0.000158489 166 1 +1124 A G 0.000158489 167 1 +1125 A F 0.000199526 168 1 +1126 G G 0.000158489 169 1 +1127 A G 0.000158489 170 1 +1128 T F 0.000199526 171 1 +1129 G B 0.000501187 172 1 +1130 G G 0.000158489 173 1 +1131 A G 0.000158489 174 1 +1132 T F 0.000199526 175 1 +1133 A G 0.000158489 176 1 +1134 A F 0.000199526 177 1 +1135 T G 0.000158489 178 1 +1136 C D 0.000316228 179 1 +1137 C G 0.000158489 180 1 +1138 T G 0.000158489 181 1 +1139 G F 0.000199526 182 1 +1140 G G 0.000158489 183 1 +1141 G G 0.000158489 184 1 +1142 A F 0.000199526 185 1 +1143 T G 0.000158489 186 1 +1144 T G 0.000158489 187 1 +1145 A G 0.000158489 188 1 +1146 A G 0.000158489 189 1 +1147 A G 0.000158489 190 1 +1148 T G 0.000158489 191 1 +1149 A G 0.000158489 192 1 +1150 A G 0.000158489 193 1 +1151 A G 0.000158489 194 1 +1152 A G 0.000158489 195 1 +1153 T G 0.000158489 196 1 +1154 A G 0.000158489 197 1 +1155 G G 0.000158489 198 1 +1156 T G 0.000158489 199 1 +1157 A G 0.000158489 200 1 +1158 A G 0.000158489 201 1 +1159 G G 0.000158489 202 1 +1160 A G 0.000158489 203 1 +1161 A 0 0.0316228 204 1 +1162 T G 0.000158489 205 1 +1163 G F 0.000199526 206 1 +1164 T G 0.000158489 207 1 +1165 A G 0.000158489 208 1 +1166 T G 0.000158489 209 1 +1167 A G 0.000158489 210 1 +1168 G G 0.000158489 211 1 +1169 C . 0.0501187 212 1 +1170 C G 0.000158489 213 1 +1171 C G 0.000158489 214 1 +1172 T G 0.000158489 215 1 +1173 A G 0.000158489 216 1 +1174 C G 0.000158489 217 1 +1175 C F 0.000199526 218 1 +1176 A G 0.000158489 219 1 +1177 G G 0.000158489 220 1 +1178 C G 0.000158489 221 1 +1179 A G 0.000158489 222 1 +1180 T F 0.000199526 223 1 +1181 T B 0.000501187 224 1 +1182 C G 0.000158489 225 1 +1183 T G 0.000158489 226 1 +1184 G G 0.000158489 227 1 +1185 G F 0.000199526 228 1 +1186 A F 0.000199526 229 1 +1187 C F 0.000199526 230 1 +1188 A F 0.000199526 231 1 +1189 T F 0.000199526 232 1 +1190 A B 0.000501187 233 1 +1191 A F 0.000199526 234 1 +1192 G F 0.000199526 235 1 +1193 A F 0.000199526 236 1 +1194 C > 0.00125893 237 1 +1195 A G 0.000158489 238 1 +1196 A 3 0.0158489 239 1 +1197 G F 0.000199526 240 1 +1198 G F 0.000199526 241 1 +1199 A G 0.000158489 242 1 +1200 C F 0.000199526 243 1 +1201 C G 0.000158489 244 1 +1202 A G 0.000158489 245 1 +1203 A G 0.000158489 246 1 +1204 A B 0.000501187 247 1 +1205 G G 0.000158489 248 1 +1206 G B 0.000501187 249 1 diff --git a/test/data/simulation/unit_data/alignment_sample03.txt b/test/data/simulation/unit_data/alignment_sample03.txt new file mode 100644 index 0000000..19f5199 --- /dev/null +++ b/test/data/simulation/unit_data/alignment_sample03.txt @@ -0,0 +1,510 @@ +SimSeq_ht1_1def +352 +601 +9204 +702 +951 +9214 +6.54289e-125 +0 +500 +352 C B 0.000501187 0 0 +353 A G 0.000158489 1 0 +354 G F 0.000199526 2 0 +355 T 0 0.0316228 3 0 +356 A @ 0.000794328 4 0 +357 T 0 0.0316228 5 0 +358 T F 0.000199526 6 0 +359 A 3 0.0158489 7 0 +360 A G 0.000158489 8 0 +361 G F 0.000199526 9 0 +362 C G 0.000158489 10 0 +363 G G 0.000158489 11 0 +364 G G 0.000158489 12 0 +365 G D 0.000316228 13 0 +366 G G 0.000158489 14 0 +367 G . 0.0501187 15 0 +368 A F 0.000199526 16 0 +369 G B 0.000501187 17 0 +370 A F 0.000199526 18 0 +371 A G 0.000158489 19 0 +372 T F 0.000199526 20 0 +373 T F 0.000199526 21 0 +374 A G 0.000158489 22 0 +375 G F 0.000199526 23 0 +376 A G 0.000158489 24 0 +377 T G 0.000158489 25 0 +378 C G 0.000158489 26 0 +379 G G 0.000158489 27 0 +380 A G 0.000158489 28 0 +381 T F 0.000199526 29 0 +382 G G 0.000158489 30 0 +383 G G 0.000158489 31 0 +384 G G 0.000158489 32 0 +385 A G 0.000158489 33 0 +386 A G 0.000158489 34 0 +387 A G 0.000158489 35 0 +388 A G 0.000158489 36 0 +389 A G 0.000158489 37 0 +390 A G 0.000158489 38 0 +391 T G 0.000158489 39 0 +392 T G 0.000158489 40 0 +393 C G 0.000158489 41 0 +394 G F 0.000199526 42 0 +395 G G 0.000158489 43 0 +396 T G 0.000158489 44 0 +397 T G 0.000158489 45 0 +398 A G 0.000158489 46 0 +399 A G 0.000158489 47 0 +400 G G 0.000158489 48 0 +401 G F 0.000199526 49 0 +402 C G 0.000158489 50 0 +403 C F 0.000199526 51 0 +404 A F 0.000199526 52 0 +405 G F 0.000199526 53 0 +406 G G 0.000158489 54 0 +407 G G 0.000158489 55 0 +408 G F 0.000199526 56 0 +409 G F 0.000199526 57 0 +410 A G 0.000158489 58 0 +411 A G 0.000158489 59 0 +412 A G 0.000158489 60 0 +413 G G 0.000158489 61 0 +414 A G 0.000158489 62 0 +415 A G 0.000158489 63 0 +416 A G 0.000158489 64 0 +417 A G 0.000158489 65 0 +418 A F 0.000199526 66 0 +419 A G 0.000158489 67 0 +420 T G 0.000158489 68 0 +421 A G 0.000158489 69 0 +422 T 1 0.0251189 70 0 +423 A G 0.000158489 71 0 +424 A G 0.000158489 72 0 +425 A G 0.000158489 73 0 +426 T G 0.000158489 74 0 +427 T G 0.000158489 75 0 +428 A G 0.000158489 76 0 +429 A G 0.000158489 77 0 +430 A G 0.000158489 78 0 +431 A G 0.000158489 79 0 +432 C G 0.000158489 80 0 +433 A F 0.000199526 81 0 +434 T G 0.000158489 82 0 +435 A G 0.000158489 83 0 +436 T G 0.000158489 84 0 +437 A G 0.000158489 85 0 +438 G G 0.000158489 86 0 +439 T G 0.000158489 87 0 +440 A I 0.0001 88 0 +441 T G 0.000158489 89 0 +442 G G 0.000158489 90 0 +443 G D 0.000316228 91 0 +444 G G 0.000158489 92 0 +445 C F 0.000199526 93 0 +446 A G 0.000158489 94 0 +447 A G 0.000158489 95 0 +448 G G 0.000158489 96 0 +449 C F 0.000199526 97 0 +450 A G 0.000158489 98 0 +451 G G 0.000158489 99 0 +452 G G 0.000158489 100 0 +453 G G 0.000158489 101 0 +454 A G 0.000158489 102 0 +455 G G 0.000158489 103 0 +456 C F 0.000199526 104 0 +457 T G 0.000158489 105 0 +458 A G 0.000158489 106 0 +459 G G 0.000158489 107 0 +460 A G 0.000158489 108 0 +461 A G 0.000158489 109 0 +462 C G 0.000158489 110 0 +463 G I 0.0001 111 0 +464 A G 0.000158489 112 0 +465 T G 0.000158489 113 0 +466 T F 0.000199526 114 0 +467 C G 0.000158489 115 0 +468 G F 0.000199526 116 0 +469 C G 0.000158489 117 0 +470 A F 0.000199526 118 0 +471 G G 0.000158489 119 0 +472 T G 0.000158489 120 0 +473 T G 0.000158489 121 0 +474 A G 0.000158489 122 0 +475 A G 0.000158489 123 0 +476 T G 0.000158489 124 0 +477 C G 0.000158489 125 0 +478 C G 0.000158489 126 0 +479 T G 0.000158489 127 0 +480 G G 0.000158489 128 0 +481 G G 0.000158489 129 0 +482 C G 0.000158489 130 0 +483 C G 0.000158489 131 0 +484 T G 0.000158489 132 0 +485 G G 0.000158489 133 0 +486 T G 0.000158489 134 0 +487 T G 0.000158489 135 0 +488 A G 0.000158489 136 0 +489 G F 0.000199526 137 0 +490 A G 0.000158489 138 0 +491 A G 0.000158489 139 0 +492 A G 0.000158489 140 0 +493 C G 0.000158489 141 0 +494 A G 0.000158489 142 0 +495 T G 0.000158489 143 0 +496 C G 0.000158489 144 0 +497 A F 0.000199526 145 0 +498 G G 0.000158489 146 0 +499 A G 0.000158489 147 0 +500 A G 0.000158489 148 0 +501 G G 0.000158489 149 0 +502 G F 0.000199526 150 0 +503 C D 0.000316228 151 0 +504 T G 0.000158489 152 0 +505 G F 0.000199526 153 0 +506 T F 0.000199526 154 0 +507 A G 0.000158489 155 0 +508 G G 0.000158489 156 0 +509 A G 0.000158489 157 0 +510 C G 0.000158489 158 0 +511 A G 0.000158489 159 0 +512 A G 0.000158489 160 0 +513 A F 0.000199526 161 0 +514 T F 0.000199526 162 0 +515 A G 0.000158489 163 0 +516 C G 0.000158489 164 0 +517 T G 0.000158489 165 0 +518 G G 0.000158489 166 0 +519 G G 0.000158489 167 0 +520 G G 0.000158489 168 0 +521 A F 0.000199526 169 0 +522 C G 0.000158489 170 0 +523 A G 0.000158489 171 0 +524 G G 0.000158489 172 0 +525 C G 0.000158489 173 0 +526 T G 0.000158489 174 0 +527 A G 0.000158489 175 0 +528 C G 0.000158489 176 0 +529 A G 0.000158489 177 0 +530 A G 0.000158489 178 0 +531 C G 0.000158489 179 0 +532 C G 0.000158489 180 0 +533 A G 0.000158489 181 0 +534 T G 0.000158489 182 0 +535 C G 0.000158489 183 0 +536 C G 0.000158489 184 0 +537 C G 0.000158489 185 0 +538 T G 0.000158489 186 0 +539 T G 0.000158489 187 0 +540 C F 0.000199526 188 0 +541 A G 0.000158489 189 0 +542 G D 0.000316228 190 0 +543 A G 0.000158489 191 0 +544 C G 0.000158489 192 0 +545 A G 0.000158489 193 0 +546 G 0 0.0316228 194 0 +547 G F 0.000199526 195 0 +548 A G 0.000158489 196 0 +549 T F 0.000199526 197 0 +550 C G 0.000158489 198 0 +551 A G 0.000158489 199 0 +552 G G 0.000158489 200 0 +553 A G 0.000158489 201 0 +554 A F 0.000199526 202 0 +555 G - 0.0630957 203 0 +556 A F 0.000199526 204 0 +557 A G 0.000158489 205 0 +558 C G 0.000158489 206 0 +559 T G 0.000158489 207 0 +560 T G 0.000158489 208 0 +561 A F 0.000199526 209 0 +562 G G 0.000158489 210 0 +563 A F 0.000199526 211 0 +564 T G 0.000158489 212 0 +565 C G 0.000158489 213 0 +566 A G 0.000158489 214 0 +567 T G 0.000158489 215 0 +568 T G 0.000158489 216 0 +569 A F 0.000199526 217 0 +570 T G 0.000158489 218 0 +571 A F 0.000199526 219 0 +572 T F 0.000199526 220 0 +573 A G 0.000158489 221 0 +574 A G 0.000158489 222 0 +575 T G 0.000158489 223 0 +576 A F 0.000199526 224 0 +577 C G 0.000158489 225 0 +578 A F 0.000199526 226 0 +579 G G 0.000158489 227 0 +580 T 0 0.0316228 228 0 +581 A F 0.000199526 229 0 +582 G F 0.000199526 230 0 +583 C F 0.000199526 231 0 +584 A G 0.000158489 232 0 +585 A F 0.000199526 233 0 +586 C F 0.000199526 234 0 +587 C F 0.000199526 235 0 +588 C F 0.000199526 236 0 +589 T F 0.000199526 237 0 +590 C F 0.000199526 238 0 +591 T A 0.000630957 239 0 +592 A G 0.000158489 240 0 +593 T F 0.000199526 241 0 +594 T F 0.000199526 242 0 +595 G F 0.000199526 243 0 +596 T B 0.000501187 244 0 +597 G F 0.000199526 245 0 +598 T F 0.000199526 246 0 +599 G A 0.000630957 247 0 +600 C B 0.000501187 248 0 +601 A A 0.000630957 249 0 +702 G F 0.000199526 0 1 +703 G ; 0.00251189 1 1 +704 A B 0.000501187 2 1 +705 C B 0.000501187 3 1 +706 A F 0.000199526 4 1 +707 C A 0.000630957 5 1 +708 A A 0.000630957 6 1 +709 G D 0.000316228 7 1 +710 C F 0.000199526 8 1 +711 A F 0.000199526 9 1 +712 A F 0.000199526 10 1 +713 T F 0.000199526 11 1 +714 C F 0.000199526 12 1 +715 A F 0.000199526 13 1 +716 G F 0.000199526 14 1 +717 G F 0.000199526 15 1 +718 T F 0.000199526 16 1 +719 C F 0.000199526 17 1 +720 A F 0.000199526 18 1 +721 G F 0.000199526 19 1 +722 C F 0.000199526 20 1 +723 C G 0.000158489 21 1 +724 A F 0.000199526 22 1 +725 A F 0.000199526 23 1 +726 A G 0.000158489 24 1 +727 A G 0.000158489 25 1 +728 T G 0.000158489 26 1 +729 T G 0.000158489 27 1 +730 A G 0.000158489 28 1 +731 C F 0.000199526 29 1 +732 C F 0.000199526 30 1 +733 C G 0.000158489 31 1 +734 T G 0.000158489 32 1 +735 A F 0.000199526 33 1 +736 T G 0.000158489 34 1 +737 A F 0.000199526 35 1 +738 G G 0.000158489 36 1 +739 T G 0.000158489 37 1 +740 G F 0.000199526 38 1 +741 C G 0.000158489 39 1 +742 A G 0.000158489 40 1 +743 G G 0.000158489 41 1 +744 A G 0.000158489 42 1 +745 A G 0.000158489 43 1 +746 C F 0.000199526 44 1 +747 A F 0.000199526 45 1 +748 T G 0.000158489 46 1 +749 C G 0.000158489 47 1 +750 C F 0.000199526 48 1 +751 A F 0.000199526 49 1 +752 G A 0.000630957 50 1 +753 G G 0.000158489 51 1 +754 G F 0.000199526 52 1 +755 G F 0.000199526 53 1 +756 C D 0.000316228 54 1 +757 A G 0.000158489 55 1 +758 A G 0.000158489 56 1 +759 A G 0.000158489 57 1 +760 T F 0.000199526 58 1 +761 G G 0.000158489 59 1 +762 G G 0.000158489 60 1 +763 T G 0.000158489 61 1 +764 A G 0.000158489 62 1 +765 C G 0.000158489 63 1 +766 A G 0.000158489 64 1 +767 T G 0.000158489 65 1 +768 C G 0.000158489 66 1 +769 A G 0.000158489 67 1 +770 G G 0.000158489 68 1 +771 G F 0.000199526 69 1 +772 C G 0.000158489 70 1 +773 C G 0.000158489 71 1 +774 A G 0.000158489 72 1 +775 T G 0.000158489 73 1 +776 A G 0.000158489 74 1 +777 T F 0.000199526 75 1 +778 C G 0.000158489 76 1 +779 A F 0.000199526 77 1 +780 C F 0.000199526 78 1 +781 C G 0.000158489 79 1 +782 T G 0.000158489 80 1 +783 A G 0.000158489 81 1 +784 G F 0.000199526 82 1 +785 A G 0.000158489 83 1 +786 A F 0.000199526 84 1 +787 C G 0.000158489 85 1 +788 T G 0.000158489 86 1 +789 T G 0.000158489 87 1 +790 T G 0.000158489 88 1 +791 A G 0.000158489 89 1 +792 A G 0.000158489 90 1 +793 A G 0.000158489 91 1 +794 T G 0.000158489 92 1 +795 G G 0.000158489 93 1 +796 C G 0.000158489 94 1 +797 A G 0.000158489 95 1 +798 T G 0.000158489 96 1 +799 G F 0.000199526 97 1 +800 G G 0.000158489 98 1 +801 G F 0.000199526 99 1 +802 T G 0.000158489 100 1 +803 A G 0.000158489 101 1 +804 A G 0.000158489 102 1 +805 A G 0.000158489 103 1 +806 A G 0.000158489 104 1 +807 G G 0.000158489 105 1 +808 T G 0.000158489 106 1 +809 A G 0.000158489 107 1 +810 G G 0.000158489 108 1 +811 T G 0.000158489 109 1 +812 A F 0.000199526 110 1 +813 G G 0.000158489 111 1 +814 A F 0.000199526 112 1 +815 A G 0.000158489 113 1 +816 G G 0.000158489 114 1 +817 A F 0.000199526 115 1 +818 G G 0.000158489 116 1 +819 A G 0.000158489 117 1 +820 A G 0.000158489 118 1 +821 G G 0.000158489 119 1 +822 G F 0.000199526 120 1 +823 C G 0.000158489 121 1 +824 T G 0.000158489 122 1 +825 T G 0.000158489 123 1 +826 T F 0.000199526 124 1 +827 C G 0.000158489 125 1 +828 A G 0.000158489 126 1 +829 G F 0.000199526 127 1 +830 C G 0.000158489 128 1 +831 C G 0.000158489 129 1 +832 C G 0.000158489 130 1 +833 A G 0.000158489 131 1 +834 G G 0.000158489 132 1 +835 A G 0.000158489 133 1 +836 A D 0.000316228 134 1 +837 G A 0.000630957 135 1 +838 T D 0.000316228 136 1 +839 G G 0.000158489 137 1 +840 A G 0.000158489 138 1 +841 T F 0.000199526 139 1 +842 A G 0.000158489 140 1 +843 C G 0.000158489 141 1 +844 C G 0.000158489 142 1 +845 C @ 0.000794328 143 1 +846 A 3 0.0158489 144 1 +847 T @ 0.000794328 145 1 +848 G G 0.000158489 146 1 +849 T G 0.000158489 147 1 +850 T G 0.000158489 148 1 +851 T G 0.000158489 149 1 +852 T G 0.000158489 150 1 +853 C G 0.000158489 151 1 +854 A G 0.000158489 152 1 +855 G G 0.000158489 153 1 +856 C F 0.000199526 154 1 +857 A G 0.000158489 155 1 +858 T G 0.000158489 156 1 +859 T G 0.000158489 157 1 +860 A F 0.000199526 158 1 +861 T G 0.000158489 159 1 +862 C . 0.0501187 160 1 +863 A F 0.000199526 161 1 +864 G G 0.000158489 162 1 +865 A G 0.000158489 163 1 +866 A G 0.000158489 164 1 +867 G F 0.000199526 165 1 +868 G G 0.000158489 166 1 +869 A G 0.000158489 167 1 +870 G G 0.000158489 168 1 +871 C G 0.000158489 169 1 +872 C G 0.000158489 170 1 +873 A G 0.000158489 171 1 +874 C 1 0.0251189 172 1 +875 C F 0.000199526 173 1 +876 C G 0.000158489 174 1 +877 C G 0.000158489 175 1 +878 A G 0.000158489 176 1 +879 C F 0.000199526 177 1 +880 A G 0.000158489 178 1 +881 A G 0.000158489 179 1 +882 G G 0.000158489 180 1 +883 A G 0.000158489 181 1 +884 T G 0.000158489 182 1 +885 T G 0.000158489 183 1 +886 T F 0.000199526 184 1 +887 A G 0.000158489 185 1 +888 A G 0.000158489 186 1 +889 A F 0.000199526 187 1 +890 C G 0.000158489 188 1 +891 A B 0.000501187 189 1 +892 C F 0.000199526 190 1 +893 C D 0.000316228 191 1 +894 A G 0.000158489 192 1 +895 T G 0.000158489 193 1 +896 G G 0.000158489 194 1 +897 C G 0.000158489 195 1 +898 T G 0.000158489 196 1 +899 A G 0.000158489 197 1 +900 A A 0.000630957 198 1 +901 A G 0.000158489 199 1 +902 C G 0.000158489 200 1 +903 A D 0.000316228 201 1 +904 C G 0.000158489 202 1 +905 A G 0.000158489 203 1 +906 G G 0.000158489 204 1 +907 T G 0.000158489 205 1 +908 G G 0.000158489 206 1 +909 G G 0.000158489 207 1 +910 G G 0.000158489 208 1 +911 G F 0.000199526 209 1 +912 G F 0.000199526 210 1 +913 G G 0.000158489 211 1 +914 A G 0.000158489 212 1 +915 C G 0.000158489 213 1 +916 A G 0.000158489 214 1 +917 T G 0.000158489 215 1 +918 C G 0.000158489 216 1 +919 A G 0.000158489 217 1 +920 A G 0.000158489 218 1 +921 G G 0.000158489 219 1 +922 C F 0.000199526 220 1 +923 A G 0.000158489 221 1 +924 G G 0.000158489 222 1 +925 C 9 0.00398107 223 1 +926 C G 0.000158489 224 1 +927 A G 0.000158489 225 1 +928 T G 0.000158489 226 1 +929 G G 0.000158489 227 1 +930 C G 0.000158489 228 1 +931 A F 0.000199526 229 1 +932 C . 0.0501187 230 1 +933 A G 0.000158489 231 1 +934 T G 0.000158489 232 1 +935 G D 0.000316228 233 1 +936 T F 0.000199526 234 1 +937 T F 0.000199526 235 1 +938 A F 0.000199526 236 1 +939 A F 0.000199526 237 1 +940 A F 0.000199526 238 1 +941 A G 0.000158489 239 1 +942 G G 0.000158489 240 1 +943 A F 0.000199526 241 1 +944 G F 0.000199526 242 1 +945 A F 0.000199526 243 1 +946 C A 0.000630957 244 1 +947 C G 0.000158489 245 1 +948 A A 0.000630957 246 1 +949 T B 0.000501187 247 1 +950 C G 0.000158489 248 1 +951 A A 0.000630957 249 1 diff --git a/test/unit/unit2.cpp b/test/unit/unit2.cpp index c3b209c..9568ae9 100644 --- a/test/unit/unit2.cpp +++ b/test/unit/unit2.cpp @@ -1,26 +1,24 @@ #include "gtest/gtest.h" #include -//#include -//#include #include #include #include "AlignmentRecord.h" #include "NewEdgeCalculator.h" -//#include + using namespace std; using namespace boost; -// This test verifies if the algorithm considers an edge between twp identical AlignmentRecords. -TEST(edgeBetweenFunctionTest, edgeBetweenSameAlignmentRecord){ +// This test verifies if the algorithm considers an edge between two identical AlignmentRecords. +TEST(edgeBetweenFunctionTest, edgeBetweenSameAlignments){ AlignmentRecord alignment; EdgeCalculator* edge_calculator = nullptr; - alignment.restoreAlignmentRecord("test/data/simulation/unit_data/alignment_sample.txt"); + alignment.restoreAlignmentRecord("test/data/simulation/unit_data/alignment_sample00.txt"); double Q = 0.9; double edge_quasi_cutoff_cliques = 0.99; @@ -42,4 +40,79 @@ TEST(edgeBetweenFunctionTest, edgeBetweenSameAlignmentRecord){ delete edge_calculator; } +// This test verifies if the algorithm considers an edge between two non_overlapping AlignmentRecords. +TEST(edgeBetweenFunctionTest, edgeBetweenNonOverlappingAlignments){ + + AlignmentRecord alignment1; + AlignmentRecord alignment2; + EdgeCalculator* edge_calculator = nullptr; + try{ + alignment1.restoreAlignmentRecord("test/data/simulation/unit_data/alignment_sample01.txt"); + }catch (...){ + cout << "File not found!" << endl; + } + + try{ + alignment2.restoreAlignmentRecord("test/data/simulation/unit_data/alignment_sample02.txt"); + }catch (...){ + cout << "File 2 not found!" << endl; + } + + double Q = 0.9; + double edge_quasi_cutoff_cliques = 0.99; + double overlap_cliques = 0.9; + bool frameshift_merge = false; + std::unordered_map simpson_map; + double edge_quasi_cutoff_single = 0.95; + double overlap_single = 0.6; + double edge_quasi_cutoff_mixed = 0.97; + unsigned int maxPosition1 = 0; + bool noProb0 = false; + + edge_calculator = new NewEdgeCalculator(Q, edge_quasi_cutoff_cliques, overlap_cliques, frameshift_merge, simpson_map, edge_quasi_cutoff_single, overlap_single, edge_quasi_cutoff_mixed, maxPosition1, noProb0); + + bool set_edge = edge_calculator->edgeBetween(alignment1, alignment2); + + EXPECT_EQ(set_edge, false); + + delete edge_calculator; +} +// This test verifies if the algorithm considers an edge between two partially overlapping AlignmentRecords. +// The second pair of the first read is aligned with the first pair of second read. +TEST(edgeBetweenFunctionTest, edgeBetweenOverlappingCrossPairsAlignments){ + + AlignmentRecord alignment1; + AlignmentRecord alignment2; + EdgeCalculator* edge_calculator = nullptr; + try{ + alignment1.restoreAlignmentRecord("test/data/simulation/unit_data/alignment_sample00.txt"); + }catch (...){ + cout << "File not found!" << endl; + } + + try{ + alignment2.restoreAlignmentRecord("test/data/simulation/unit_data/alignment_sample03.txt"); + }catch (...){ + cout << "File 2 not found!" << endl; + } + + double Q = 0.9; + double edge_quasi_cutoff_cliques = 0.99; + double overlap_cliques = 0.9; + bool frameshift_merge = false; + std::unordered_map simpson_map; + double edge_quasi_cutoff_single = 0.95; + double overlap_single = 0.6; + double edge_quasi_cutoff_mixed = 0.97; + unsigned int maxPosition1 = 0; + bool noProb0 = false; + + edge_calculator = new NewEdgeCalculator(Q, edge_quasi_cutoff_cliques, overlap_cliques, frameshift_merge, simpson_map, edge_quasi_cutoff_single, overlap_single, edge_quasi_cutoff_mixed, maxPosition1, noProb0); + + bool set_edge = edge_calculator->edgeBetween(alignment1, alignment2); + + EXPECT_EQ(set_edge, false); + + delete edge_calculator; +}