b31907d700c1fe956e4e4c20e64d91de027d7c84 markd Tue May 14 02:03:33 2024 -0700 merge blatHuge implementation diff --git src/gfClient/tests/expected/repeat.psl src/gfClient/tests/expected/repeat.psl new file mode 100644 index 0000000..673e3a4 --- /dev/null +++ src/gfClient/tests/expected/repeat.psl @@ -0,0 +1,89 @@ +266 23 0 0 0 0 0 0 + alu 290 0 289 chr1 248956422 2056730 2057019 1 289, 0, 2056730, +265 21 0 0 0 0 0 0 + alu 290 0 286 chr1 248956422 25822528 25822814 1 286, 0, 25822528, +214 19 0 0 2 57 2 59 + alu 290 0 290 chr1 248956422 26241244 26241536 3 37,80,116, 0,91,174, 26241244,26241335,26241420, +234 16 0 0 1 7 3 385 + alu 290 32 289 chr1 248956422 55221246 55221881 4 25,89,6,130, 32,57,146,159, 55221246,55221649,55221741,55221751, +247 19 0 0 0 0 1 1 + alu 290 9 275 chr1 248956422 147829986 147830253 2 156,110, 9,165, 147829986,147830143, +253 18 0 0 1 4 2 15 + alu 290 9 284 chr1 248956422 171481329 171481615 3 8,212,51, 9,21,233, 171481329,171481350,171481564, +252 22 0 0 1 1 3 60 + alu 290 0 275 chr1 248956422 191123410 191123744 5 12,25,4,25,208, 0,12,38,42,67, 191123410,191123480,191123505,191123510,191123536, +263 18 0 0 1 8 4 12 + alu 290 0 289 chr1 248956422 202136854 202137147 5 9,136,7,5,124, 0,9,145,160,165, 202136854,202136865,202137004,202137016,202137023, +250 27 0 0 0 0 0 0 + alu 290 12 289 chr1 248956422 246788469 246788746 1 277, 12, 246788469, +252 23 0 0 0 0 1 1 + alu 290 0 275 chr10 133797422 28804156 28804432 2 165,110, 0,165, 28804156,28804322, +261 21 0 0 0 0 0 0 + alu 290 4 286 chr10 133797422 74029119 74029401 1 282, 4, 74029119, +245 20 0 0 3 19 5 37 + alu 290 4 288 chr10 133797422 119645565 119645867 6 33,97,7,5,9,114, 4,45,145,160,165,174, 119645565,119645613,119645716,119645728,119645742,119645753, +223 19 0 0 0 0 0 0 + alu 290 45 287 chr11 135086622 5730238 5730480 1 242, 45, 5730238, +255 24 0 0 2 2 0 0 + alu 290 9 290 chr11 135086622 40006700 40006979 3 7,44,228, 9,17,62, 40006700,40006707,40006751, +258 27 0 0 0 0 0 0 + alu 290 4 289 chr11 135086622 46964291 46964576 1 285, 4, 46964291, +253 28 0 0 0 0 1 8 + alu 290 9 290 chr11 135086622 81728313 81728602 2 10,271, 9,19, 81728313,81728331, +265 19 0 0 1 1 2 20 + alu 290 4 289 chr11 135086622 113165818 113166122 3 104,63,117, 4,108,172, 113165818,113165929,113166005, +252 23 0 0 2 10 2 10 + alu 290 4 289 chr11 135086622 130140912 130141197 3 138,7,130, 4,145,159, 130140912,130141056,130141067, +234 21 0 0 2 31 2 7 + alu 290 0 286 chr12 133275309 32793621 32793883 4 18,103,7,127, 0,42,145,159, 32793621,32793639,32793745,32793756, +258 20 0 0 1 7 2 7 + alu 290 0 285 chr12 133275309 34148263 34148548 3 18,149,111, 0,25,174, 34148263,34148287,34148437, +243 13 0 0 0 0 2 2 + alu 290 29 285 chr12 133275309 50499204 50499462 3 142,3,111, 29,171,174, 50499204,50499347,50499351, +260 22 0 0 2 7 3 8 + alu 290 0 289 chr12 133275309 56853113 56853403 5 13,129,7,4,129, 0,13,145,152,160, 56853113,56853127,56853262,56853270,56853274, +262 22 0 0 1 5 2 18 + alu 290 0 289 chr13 114364328 22855245 22855547 3 16,150,118, 0,21,171, 22855245,22855277,22855429, +253 25 0 0 1 1 1 1 + alu 290 11 290 chr13 114364328 61436333 61436612 3 26,4,248, 11,38,42, 61436333,61436359,61436364, +219 20 0 0 1 9 3 10 + alu 290 42 290 chr14 107043718 28840830 28841079 4 104,5,11,119, 42,146,160,171, 28840830,28840937,28840948,28840960, +263 23 0 0 0 0 0 0 + alu 290 0 286 chr14 107043718 84730056 84730342 1 286, 0, 84730056, +290 0 0 0 0 0 0 0 + alu 290 0 290 chr22 50818468 38876790 38877080 1 290, 0, 38876790, +251 25 0 0 1 1 0 0 + alu 290 12 289 chr2_KN538363v1_fix 365499 157379 157655 2 153,123, 12,166, 157379,157532, +239 21 0 0 0 0 0 0 + alu 290 0 260 chr3 198295559 7200971 7201231 1 260, 0, 7200971, +265 22 0 0 0 0 1 1 + alu 290 0 287 chr3 198295559 23847496 23847784 2 173,114, 0,173, 23847496,23847670, +265 19 0 0 0 0 1 1 + alu 290 0 284 chr3 198295559 28974492 28974777 2 171,113, 0,171, 28974492,28974664, +255 22 0 0 2 9 3 10 + alu 290 0 286 chr3 198295559 32691163 32691450 4 144,6,113,14, 0,145,159,272, 32691163,32691311,32691322,32691436, +57 1 0 0 1 81 1 83 + alu 290 148 287 chr3 198295559 47052321 47052462 2 21,37, 148,250, 47052321,47052425, +255 22 0 0 2 9 3 10 + alu 290 0 286 chr3_MU273347v1_fix 301310 59389 59676 4 144,6,113,14, 0,145,159,272, 59389,59537,59548,59662, +249 19 0 0 3 17 3 13 + alu 290 4 289 chr4 190214555 77668940 77669221 6 22,61,15,119,13,38, 4,30,92,107,226,251, 77668940,77668962,77669023,77669039,77669159,77669183, +191 15 0 0 1 1 0 0 + alu 290 68 275 chr4 190214555 97532952 97533158 2 97,109, 68,166, 97532952,97533049, +251 27 0 0 0 0 0 0 + alu 290 11 289 chr5 181538259 91338548 91338826 1 278, 11, 91338548, +240 14 0 0 2 9 2 9 + alu 290 0 263 chr8 145138636 642346 642609 3 142,7,105, 0,145,158, 642346,642494,642504, +243 19 0 0 2 20 3 12 + alu 290 4 286 chr8 145138636 6404248 6404522 4 141,7,105,9, 4,145,158,277, 6404248,6404392,6404402,6404513, +265 24 0 0 0 0 1 2 + alu 290 0 289 chr8 145138636 85180579 85180870 2 165,124, 0,165, 85180579,85180746, +262 26 0 0 0 0 0 0 + alu 290 0 288 chr9 138394717 128948727 128949015 1 288, 0, 128948727, +240 12 0 0 3 11 2 10 + alu 290 26 289 chrX 156040895 23889690 23889952 4 98,17,7,130, 26,125,145,159, 23889690,23889788,23889811,23889822, +240 22 0 0 1 25 1 42 - alu 290 0 287 chr1 248956422 39359698 39360002 2 120,142, 3,148, 39359698,39359860, +256 26 0 0 0 0 0 0 - alu 290 4 286 chr1 248956422 42052876 42053158 1 282, 4, 42052876, +255 21 0 0 2 10 4 16 - alu 290 0 286 chr1 248956422 64221815 64222107 5 96,14,3,104,59, 4,102,116,119,231, 64221815,64221912,64221927,64221931,64222048, +267 22 0 0 1 1 0 0 - alu 290 0 290 chr1 248956422 66519237 66519526 2 281,8, 0,282, 66519237,66519518, +254 25 0 0 0 0 0 0 - alu 290 9 288 chr1 248956422 77773185 77773464 1 279, 2, 77773185, +259 28 0 0 0 0 0 0 - alu 290 0 287 chr1 248956422 147976962 147977249 1 287, 3, 147976962, +259 21 0 0 3 9 2 6 - alu 290 0 289 chr1 248956422 163243373 163243659 4 43,4,166,67, 1,45,51,223, 163243373,163243416,163243423,163243592, +257 20 0 0 1 6 3 15 - alu 290 4 287 chr1 248956422 172858940 172859232 4 113,9,143,12, 3,116,125,274, 172858940,172859054,172859064,172859220, +256 20 0 0 1 4 1 5 - alu 290 4 284 chr1 248956422 211070149 211070430 2 264,12, 6,274, 211070149,211070418, +263 26 0 0 0 0 1 1 - alu 290 0 289 chr1 248956422 216465277 216465567 2 124,165, 1,125, 216465277,216465402, +228 25 0 0 0 0 1 1 - alu 290 37 290 chr10 133797422 1023200 1023454 2 125,128, 0,125, 1023200,1023326, +253 21 0 0 1 1 0 0 - alu 290 0 275 chr10 133797422 61856166 61856440 2 254,20, 15,270, 61856166,61856420, +263 26 0 0 0 0 0 0 - alu 290 0 289 chr10 133797422 69998553 69998842 1 289, 1, 69998553, +220 23 0 0 0 0 0 0 - alu 290 45 288 chr10 133797422 86358485 86358728 1 243, 2, 86358485, +261 25 0 0 0 0 1 4 - alu 290 4 290 chr10 133797422 95897404 95897694 2 115,171, 0,115, 95897404,95897523, +246 20 0 0 3 22 3 30 - alu 290 0 288 chr10 133797422 113727711 113728007 4 39,6,67,154, 2,46,58,136, 113727711,113727751,113727767,113727853, +264 21 0 0 1 1 1 1 - alu 290 0 286 chr11 135086622 24152394 24152680 3 121,144,20, 4,125,270, 24152394,24152516,24152660, +251 21 0 0 1 6 2 8 - alu 290 11 289 chr11 135086622 33225943 33226223 3 9,109,154, 1,16,125, 33225943,33225959,33226069, +204 20 0 0 1 1 0 0 - alu 290 61 286 chr11 135086622 32640746 32640970 2 170,54, 4,175, 32640746,32640916, +110 10 0 0 1 11 1 12 - alu 290 4 135 chr11 135086622 57442736 57442868 2 98,22, 155,264, 57442736,57442846, +262 23 0 0 1 1 2 312 - alu 290 0 286 chr11 135086622 102264261 102264858 4 225,3,49,8, 4,229,232,282, 102264261,102264508,102264801,102264850, +261 28 0 0 0 0 0 0 - alu 290 1 290 chr11 135086622 129936378 129936667 1 289, 0, 129936378, +209 20 0 0 0 0 0 0 - alu 290 4 233 chr12 133275309 8557947 8558176 1 229, 57, 8557947, +230 24 0 0 0 0 1 2 - alu 290 4 258 chr12 133275309 14302045 14302301 2 93,161, 32,125, 14302045,14302140, +198 19 0 0 1 1 2 149 - alu 290 68 286 chr12 133275309 57412734 57413100 4 26,95,33,63, 4,30,125,159, 57412734,57412906,57413004,57413037, +262 28 0 0 0 0 1 1 - alu 290 0 290 chr12 133275309 64226892 64227183 2 125,165, 0,125, 64226892,64227018, +263 25 0 0 0 0 0 0 - alu 290 0 288 chr15 101991189 26764857 26765145 1 288, 2, 26764857, +224 25 0 0 0 0 1 1 - alu 290 38 287 chr16 90338345 35683801 35684051 2 245,4, 3,248, 35683801,35684047, +142 7 0 0 1 35 1 37 - alu 290 102 286 chr16 90338345 72217580 72217766 2 53,96, 4,92, 72217580,72217670, +255 24 0 0 0 0 0 0 - alu 290 9 288 chr16 90338345 87018821 87019100 1 279, 2, 87018821, +263 19 0 0 2 4 0 0 - alu 290 0 286 chr17 83257441 38818322 38818604 3 60,167,55, 4,65,235, 38818322,38818382,38818549, +262 22 0 0 1 1 0 0 - alu 290 4 289 chr19 58617616 3928971 3929255 2 123,161, 1,125, 3928971,3929094, +265 24 0 0 0 0 0 0 - alu 290 0 289 chr19 58617616 49265434 49265723 1 289, 1, 49265434, +261 21 0 0 2 3 1 4 - alu 290 3 288 chr2 242193529 9514600 9514886 3 144,126,12, 2,148,275, 9514600,9514748,9514874, +261 29 0 0 0 0 1 1 - alu 290 0 290 chr2 242193529 79305770 79306061 2 125,165, 0,125, 79305770,79305896, +268 20 0 0 0 0 1 1 - alu 290 0 288 chr21 46709983 20374567 20374856 2 284,4, 2,286, 20374567,20374852, +256 20 0 0 2 9 3 336 - alu 290 0 285 chr21 46709983 40004937 40005549 4 156,74,12,34, 5,161,236,256, 40004937,40005415,40005494,40005515, +107 11 0 0 0 0 0 0 - alu 290 80 198 chr22 50818468 43903795 43903913 1 118, 92, 43903795, +255 23 0 0 2 7 2 11 - alu 290 4 289 chr3 198295559 52945533 52945822 4 99,23,111,45, 1,102,125,241, 52945533,52945632,52945657,52945777, +249 22 0 0 1 4 1 12 - alu 290 9 284 chr4 190214555 62285943 62286226 2 262,9, 6,272, 62285943,62286217, +265 24 0 0 0 0 1 2 - alu 290 0 289 chr5 181538259 20423671 20423962 2 124,165, 1,125, 20423671,20423797, +265 24 0 0 0 0 0 0 - alu 290 0 289 chr6 170805979 24373888 24374177 1 289, 1, 24373888, +263 25 0 0 1 2 0 0 - alu 290 0 290 chr6 170805979 52449108 52449396 2 170,118, 0,172, 52449108,52449278, +258 23 0 0 1 6 2 7 - alu 290 0 287 chr6_GL000254v2_alt 4827813 3820593 3820881 3 108,90,83, 3,111,207, 3820593,3820703,3820798, +263 22 0 0 1 1 2 10 - alu 290 4 290 chr8 145138636 24396235 24396530 3 125,152,8, 0,126,278, 24396235,24396363,24396522, +239 25 0 0 0 0 1 2 - alu 290 11 275 chr9 138394717 123901744 123902010 2 110,154, 15,125, 123901744,123901856, +238 26 0 0 0 0 0 0 - alu 290 25 289 chrX 156040895 19760113 19760377 1 264, 1, 19760113,