b31907d700c1fe956e4e4c20e64d91de027d7c84 markd Tue May 14 02:03:33 2024 -0700 merge blatHuge implementation diff --git src/gfServer/tests/expected/testHugeUntrans.psl src/gfServer/tests/expected/testHugeUntrans.psl new file mode 100644 index 0000000..1a70b6e --- /dev/null +++ src/gfServer/tests/expected/testHugeUntrans.psl @@ -0,0 +1,142 @@ +109 10 0 0 0 0 1 1 + XM_044058998.1 5509 937 1056 NC_056725.1 2000000000 203988601 203988721 2 9,110, 937,946, 203988601,203988611, +65 6 0 0 0 0 0 0 + XM_044058998.1 5509 980 1051 NC_056725.1 2000000000 488951369 488951440 1 71, 980, 488951369, +58 3 0 0 1 1 0 0 + XM_044058998.1 5509 989 1051 NC_056725.1 2000000000 687213563 687213624 2 37,24, 989,1027, 687213563,687213600, +70 7 0 0 0 0 0 0 + XM_044058998.1 5509 773 850 NC_056725.1 2000000000 728639436 728639513 1 77, 773, 728639436, +63 4 0 0 0 0 0 0 + XM_044058998.1 5509 984 1051 NC_056725.1 2000000000 872807999 872808066 1 67, 984, 872807999, +69 2 0 0 0 0 0 0 + XM_044058998.1 5509 980 1051 NC_056725.1 2000000000 926333139 926333210 1 71, 980, 926333139, +33 0 0 0 0 0 0 0 + XM_044058998.1 5509 1015 1048 NC_056725.1 2000000000 1320816568 1320816601 1 33, 1015, 1320816568, +111 9 0 0 0 0 0 0 + XM_044058998.1 5509 937 1057 NC_056725.1 2000000000 1668366056 1668366176 1 120, 937, 1668366056, +67 4 0 0 0 0 0 0 + XM_044058998.1 5509 980 1051 NC_056725.1 2000000000 1832435301 1832435372 1 71, 980, 1832435301, +44 1 0 0 0 0 0 0 + XM_044058998.1 5509 1006 1051 NC_056725.1 2000000000 1979730272 1979730317 1 45, 1006, 1979730272, +78 3 0 0 2 11 2 12 + XM_044058998.1 5509 959 1051 NC_056726.1 2000000000 1621014596 1621014689 3 29,7,45, 959,995,1006, 1621014596,1621014636,1621014644, +113 6 0 0 0 0 1 1 + XM_044058998.1 5509 937 1056 NC_056726.1 2000000000 1715101467 1715101587 2 9,110, 937,946, 1715101467,1715101477, +61 6 0 0 0 0 0 0 + XM_044058998.1 5509 984 1051 NC_056726.1 2000000000 1935681512 1935681579 1 67, 984, 1935681512, +65 4 0 0 1 3 1 3 + XM_044058998.1 5509 984 1056 NC_056727.1 1260428656 23845886 23845958 3 13,5,51, 984,997,1005, 23845886,23845902,23845907, +79 4 0 0 2 20 2 175 + XM_044058998.1 5509 950 1053 NC_056727.1 1260428656 188581078 188581336 3 16,13,54, 950,984,999, 188581078,188581111,188581282, +53 0 0 0 1 7 2 7 + XM_044058998.1 5509 987 1047 NC_056727.1 1260428656 243433805 243433865 3 8,7,38, 987,995,1009, 243433805,243433816,243433827, +50 2 0 0 0 0 0 0 + XM_044058998.1 5509 999 1051 NC_056727.1 1260428656 825313236 825313288 1 52, 999, 825313236, +84 6 0 0 1 11 2 11 + XM_044058998.1 5509 950 1051 NC_056727.1 1260428656 1029409794 1029409895 3 41,13,36, 950,1002,1015, 1029409794,1029409845,1029409859, +61 6 0 0 0 0 0 0 + XM_044058998.1 5509 984 1051 NC_056727.1 1260428656 1091814876 1091814943 1 67, 984, 1091814876, +62 5 0 0 0 0 0 0 + XM_044058998.1 5509 984 1051 NC_056727.1 1260428656 1166730871 1166730938 1 67, 984, 1166730871, +100 9 0 0 0 0 0 0 + XM_044058998.1 5509 947 1056 NC_056728.1 2000000000 1192119834 1192119943 1 109, 947, 1192119834, +63 4 0 0 0 0 0 0 + XM_044058998.1 5509 984 1051 NC_056728.1 2000000000 1211207358 1211207425 1 67, 984, 1211207358, +71 5 0 0 1 3 1 3 + XM_044058998.1 5509 977 1056 NC_056728.1 2000000000 1478759108 1478759187 3 18,7,51, 977,995,1005, 1478759108,1478759129,1478759136, +65 5 0 0 1 2 1 225 + XM_044058998.1 5509 984 1056 NC_056728.1 2000000000 1628853837 1628854132 2 13,57, 984,999, 1628853837,1628854075, +109 9 0 0 1 1 1 1 + XM_044058998.1 5509 937 1056 NC_056728.1 2000000000 1888446208 1888446327 3 9,77,32, 937,946,1024, 1888446208,1888446218,1888446295, +103 6 0 0 2 6 2 7 + XM_044058998.1 5509 937 1052 NC_056728.1 2000000000 1936038142 1936038258 4 9,46,7,47, 937,946,995,1005, 1936038142,1936038152,1936038204,1936038211, +53 0 0 0 1 7 2 7 + XM_044058998.1 5509 987 1047 NC_056729.1 2000000000 630966875 630966935 3 8,7,38, 987,995,1009, 630966875,630966886,630966897, +51 1 0 0 1 4 1 1 + XM_044058998.1 5509 995 1051 NC_056729.1 2000000000 968413337 968413390 2 7,45, 995,1006, 968413337,968413345, +63 2 0 0 1 2 1 220 + XM_044058998.1 5509 984 1051 NC_056729.1 2000000000 1131416624 1131416909 2 13,52, 984,999, 1131416624,1131416857, +57 6 0 0 0 0 0 0 + XM_044058998.1 5509 988 1051 NC_056729.1 2000000000 1354036013 1354036076 1 63, 988, 1354036013, +67 4 0 0 0 0 0 0 + XM_044058998.1 5509 980 1051 NC_056730.1 1156288062 94039185 94039256 1 71, 980, 94039185, +65 6 0 0 0 0 0 0 + XM_044058998.1 5509 980 1051 NC_056730.1 1156288062 629347064 629347135 1 71, 980, 629347064, +58 5 0 0 0 0 0 0 + XM_044058998.1 5509 984 1047 NC_056730.1 1156288062 1111839694 1111839757 1 63, 984, 1111839694, +69 5 0 0 1 18 1 26 + XM_044058998.1 5509 959 1051 NC_056731.1 2000000000 234331589 234331689 2 38,36, 959,1015, 234331589,234331653, +65 2 0 0 0 0 0 0 + XM_044058998.1 5509 984 1051 NC_056731.1 2000000000 1422833573 1422833640 1 67, 984, 1422833573, +111 7 0 0 1 1 0 0 + XM_044058998.1 5509 937 1056 NC_056731.1 2000000000 1537190090 1537190208 2 7,111, 937,945, 1537190090,1537190097, +62 5 0 0 0 0 0 0 + XM_044058998.1 5509 984 1051 NC_056731.1 2000000000 1537226364 1537226431 1 67, 984, 1537226364, +96 10 0 0 0 0 0 0 + XM_044058998.1 5509 945 1051 NC_056732.1 1916691190 761395770 761395876 1 106, 945, 761395770, +42 2 0 0 0 0 0 0 + XM_044058998.1 5509 1007 1051 NC_056732.1 1916691190 862998618 862998662 1 44, 1007, 862998618, +111 7 0 0 0 0 0 0 + XM_044058998.1 5509 939 1057 NC_056732.1 1916691190 971065336 971065454 1 118, 939, 971065336, +71 5 0 0 0 0 0 0 + XM_044058998.1 5509 980 1056 NC_056732.1 1916691190 1158284090 1158284166 1 76, 980, 1158284090, +62 5 0 0 0 0 0 0 + XM_044058998.1 5509 984 1051 NC_056732.1 1916691190 1158236599 1158236666 1 67, 984, 1158236599, +101 5 0 0 1 1 1 1 + XM_044058998.1 5509 937 1044 NC_056733.1 2000000000 1240629800 1240629907 3 9,77,20, 937,946,1024, 1240629800,1240629810,1240629887, +111 7 0 0 1 1 1 2 + XM_044058998.1 5509 937 1056 NC_056733.1 2000000000 1314066681 1314066801 2 8,110, 937,946, 1314066681,1314066691, +110 9 0 0 0 0 1 1 + XM_044058998.1 5509 937 1056 NC_056733.1 2000000000 1749577371 1749577491 2 9,110, 937,946, 1749577371,1749577381, +64 3 0 0 0 0 0 0 + XM_044058998.1 5509 984 1051 NC_056733.1 2000000000 1961969617 1961969684 1 67, 984, 1961969617, +65 6 0 0 0 0 0 0 + XM_044058998.1 5509 980 1051 NC_056734.1 1017585886 252215042 252215113 1 71, 980, 252215042, +59 4 0 0 0 0 0 0 + XM_044058998.1 5509 984 1047 NC_056735.1 2000000000 106047698 106047761 1 63, 984, 106047698, +49 3 0 0 0 0 0 0 + XM_044058998.1 5509 999 1051 NC_056735.1 2000000000 480620708 480620760 1 52, 999, 480620708, +87 4 0 0 0 0 0 0 + XM_044058998.1 5509 960 1051 NC_056735.1 2000000000 516840525 516840616 1 91, 960, 516840525, +56 4 0 0 0 0 0 0 + XM_044058998.1 5509 988 1048 NC_056735.1 2000000000 538058842 538058902 1 60, 988, 538058842, +107 8 0 0 0 0 1 1 + XM_044058998.1 5509 937 1052 NC_056736.1 813524174 9573973 9574089 2 9,106, 937,946, 9573973,9573983, +56 1 0 0 1 3 1 3 + XM_044058998.1 5509 987 1047 NC_056739.1 2000000000 1609929817 1609929877 3 8,7,42, 987,995,1005, 1609929817,1609929828,1609929835, +67 4 0 0 0 0 0 0 + XM_044058998.1 5509 980 1051 NC_056739.1 2000000000 1863422574 1863422645 1 71, 980, 1863422574, +111 8 0 0 1 1 0 0 + XM_044058998.1 5509 937 1057 NC_056742.1 549370250 209271836 209271955 2 54,65, 937,992, 209271836,209271890, +105 6 0 0 0 0 1 1 + XM_044058998.1 5509 937 1048 NC_056743.1 1974114035 713103734 713103846 2 9,102, 937,946, 713103734,713103744, +104 9 0 0 1 1 1 2 + XM_044058998.1 5509 937 1051 NC_056743.1 1974114035 894445961 894446076 2 9,104, 937,947, 894445961,894445972, +47 1 0 0 0 0 0 0 + XM_044058998.1 5509 999 1047 NC_056743.1 1974114035 1132477084 1132477132 1 48, 999, 1132477084, +101 7 0 0 1 1 1 2 + XM_044058998.1 5509 948 1057 NC_056744.1 1842211721 1738591209 1738591319 2 100,8, 948,1049, 1738591209,1738591311, +63 4 0 0 0 0 0 0 + XM_044058998.1 5509 984 1051 NC_056746.1 1577849408 1367090082 1367090149 1 67, 984, 1367090082, +65 2 0 0 0 0 0 0 + XM_044058998.1 5509 984 1051 NC_056749.1 863342500 230153391 230153458 1 67, 984, 230153391, +5509 0 0 0 0 0 26 1544525 + XM_044058998.1 5509 0 5509 NC_056751.1 836063838 386479204 388029238 27 492,120,148,93,86,118,157,74,81,102,204,85,172,217,185,82,99,97,99,98,90,137,186,139,118,103,1927, 0,492,612,760,853,939,1057,1214,1288,1369,1471,1675,1760,1932,2149,2334,2416,2515,2612,2711,2809,2899,3036,3222,3361,3479,3582, 386479204,386787359,386942073,387120435,387127220,387192999,387199297,387316427,387371607,387416919,387468025,387520464,387546721,387559768,387585916,387674698,387677866,387689570,387722128,387741793,387779898,387887328,387902725,387976541,387993251,388004376,388027311, +109 7 0 0 0 0 1 1 + XM_044058998.1 5509 937 1053 NC_056751.1 836063838 496791265 496791382 2 9,107, 937,946, 496791265,496791275, +39 1 0 0 0 0 0 0 - XM_044058998.1 5509 1011 1051 NC_056725.1 2000000000 180697398 180697438 1 40, 4458, 180697398, +63 4 0 0 0 0 0 0 - XM_044058998.1 5509 984 1051 NC_056725.1 2000000000 362179676 362179743 1 67, 4458, 362179676, +64 4 0 0 0 0 0 0 - XM_044058998.1 5509 983 1051 NC_056725.1 2000000000 873696786 873696854 1 68, 4458, 873696786, +109 10 0 0 0 0 1 1 - XM_044058998.1 5509 937 1056 NC_056725.1 2000000000 905841561 905841681 2 110,9, 4453,4563, 905841561,905841672, +96 6 0 0 2 12 4 13 - XM_044058998.1 5509 937 1051 NC_056725.1 2000000000 949300435 949300550 5 35,5,7,46,9, 4458,4502,4507,4517,4563, 949300435,949300475,949300481,949300494,949300541, +62 5 0 0 0 0 0 0 - XM_044058998.1 5509 984 1051 NC_056725.1 2000000000 1243939060 1243939127 1 67, 4458, 1243939060, +114 7 0 0 0 0 0 0 - XM_044058998.1 5509 937 1058 NC_056725.1 2000000000 1299170132 1299170253 1 121, 4451, 1299170132, +110 9 0 0 0 0 1 1 - XM_044058998.1 5509 937 1056 NC_056725.1 2000000000 1475563421 1475563541 2 110,9, 4453,4563, 1475563421,1475563532, +111 8 0 0 0 0 1 1 - XM_044058998.1 5509 937 1056 NC_056725.1 2000000000 1492289124 1492289244 2 110,9, 4453,4563, 1492289124,1492289235, +106 7 0 0 2 2 2 4 - XM_044058998.1 5509 937 1052 NC_056725.1 2000000000 1729111902 1729112019 3 24,80,9, 4457,4482,4563, 1729111902,1729111928,1729112010, +79 5 0 0 0 0 0 0 - XM_044058998.1 5509 967 1051 NC_056726.1 2000000000 45270471 45270555 1 84, 4458, 45270471, +110 8 0 0 1 1 2 3 - XM_044058998.1 5509 937 1056 NC_056726.1 2000000000 589773458 589773579 3 33,77,8, 4453,4486,4564, 589773458,589773492,589773571, +57 5 0 0 0 0 0 0 - XM_044058998.1 5509 984 1046 NC_056726.1 2000000000 732838475 732838537 1 62, 4463, 732838475, +62 5 0 0 0 0 0 0 - XM_044058998.1 5509 984 1051 NC_056726.1 2000000000 828853898 828853965 1 67, 4458, 828853898, +46 1 0 0 1 3 0 0 - XM_044058998.1 5509 995 1045 NC_056727.1 1260428656 11508045 11508092 2 40,7, 4464,4507, 11508045,11508085, +51 0 0 0 1 1 0 0 - XM_044058998.1 5509 999 1051 NC_056727.1 1260428656 238707561 238707612 2 27,24, 4458,4486, 238707561,238707588, +106 9 0 0 0 0 2 4 - XM_044058998.1 5509 937 1052 NC_056727.1 1260428656 1044608815 1044608934 3 5,101,9, 4457,4462,4563, 1044608815,1044608823,1044608925, +63 4 0 0 0 0 0 0 - XM_044058998.1 5509 984 1051 NC_056727.1 1260428656 1150384146 1150384213 1 67, 4458, 1150384146, +62 5 0 0 0 0 0 0 - XM_044058998.1 5509 984 1051 NC_056728.1 2000000000 331839669 331839736 1 67, 4458, 331839669, +101 7 0 0 1 11 2 9 - XM_044058998.1 5509 937 1056 NC_056728.1 2000000000 369390867 369390984 3 72,27,9, 4453,4536,4563, 369390867,369390947,369390975, +70 3 0 0 0 0 1 7 - XM_044058998.1 5509 984 1057 NC_056728.1 2000000000 659444413 659444493 2 63,10, 4452,4515, 659444413,659444483, +109 10 0 0 0 0 2 2 - XM_044058998.1 5509 937 1056 NC_056728.1 2000000000 1520736501 1520736622 3 33,77,9, 4453,4486,4563, 1520736501,1520736535,1520736613, +66 7 0 0 0 0 0 0 - XM_044058998.1 5509 983 1056 NC_056728.1 2000000000 1536125917 1536125990 1 73, 4453, 1536125917, +67 5 0 0 0 0 0 0 - XM_044058998.1 5509 984 1056 NC_056728.1 2000000000 1687803510 1687803582 1 72, 4453, 1687803510, +110 6 0 0 1 3 2 4 - XM_044058998.1 5509 937 1056 NC_056728.1 2000000000 1784962972 1784963092 4 51,5,51,9, 4453,4507,4512,4563, 1784962972,1784963023,1784963031,1784963083, +111 9 0 0 0 0 0 0 - XM_044058998.1 5509 937 1057 NC_056728.1 2000000000 1808192733 1808192853 1 120, 4452, 1808192733, +82 6 0 0 0 0 0 0 - XM_044058998.1 5509 959 1047 NC_056728.1 2000000000 1934688914 1934689002 1 88, 4462, 1934688914, +62 5 0 0 0 0 0 0 - XM_044058998.1 5509 984 1051 NC_056729.1 2000000000 766009801 766009868 1 67, 4458, 766009801, +69 3 0 0 2 17 3 14 - XM_044058998.1 5509 962 1051 NC_056729.1 2000000000 842324178 842324264 4 45,7,6,14, 4458,4507,4514,4533, 842324178,842324224,842324234,842324250, +62 5 0 0 0 0 0 0 - XM_044058998.1 5509 984 1051 NC_056729.1 2000000000 1000157797 1000157864 1 67, 4458, 1000157797, +71 5 0 0 0 0 0 0 - XM_044058998.1 5509 980 1056 NC_056729.1 2000000000 1043266210 1043266286 1 76, 4453, 1043266210, +61 6 0 0 0 0 0 0 - XM_044058998.1 5509 984 1051 NC_056730.1 1156288062 225568600 225568667 1 67, 4458, 225568600, +103 8 0 0 1 8 1 9 - XM_044058998.1 5509 937 1056 NC_056730.1 1156288062 265853135 265853255 2 102,9, 4453,4563, 265853135,265853246, +50 2 0 0 0 0 0 0 - XM_044058998.1 5509 999 1051 NC_056730.1 1156288062 496341988 496342040 1 52, 4458, 496341988, +66 4 0 0 0 0 0 0 - XM_044058998.1 5509 981 1051 NC_056730.1 1156288062 996132702 996132772 1 70, 4458, 996132702, +112 8 0 0 0 0 0 0 - XM_044058998.1 5509 937 1057 NC_056730.1 1156288062 1001962681 1001962801 1 120, 4452, 1001962681, +58 6 0 0 0 0 0 0 - XM_044058998.1 5509 984 1048 NC_056731.1 2000000000 130359706 130359770 1 64, 4461, 130359706, +106 10 0 0 0 0 1 1 - XM_044058998.1 5509 937 1053 NC_056731.1 2000000000 694437462 694437579 2 107,9, 4456,4563, 694437462,694437570, +95 7 0 0 0 0 0 0 - XM_044058998.1 5509 937 1039 NC_056731.1 2000000000 941490343 941490445 1 102, 4470, 941490343, +63 6 0 0 0 0 0 0 - XM_044058998.1 5509 984 1053 NC_056731.1 2000000000 1298184299 1298184368 1 69, 4456, 1298184299, +42 1 0 0 0 0 0 0 - XM_044058998.1 5509 1008 1051 NC_056731.1 2000000000 1509405416 1509405459 1 43, 4458, 1509405416, +61 3 0 0 1 3 1 3 - XM_044058998.1 5509 984 1051 NC_056731.1 2000000000 1727440221 1727440288 3 46,7,11, 4458,4507,4514, 1727440221,1727440267,1727440277, +58 5 0 0 0 0 0 0 - XM_044058998.1 5509 984 1047 NC_056731.1 2000000000 1809673895 1809673958 1 63, 4462, 1809673895, +68 3 0 0 0 0 0 0 - XM_044058998.1 5509 980 1051 NC_056732.1 1916691190 911519660 911519731 1 71, 4458, 911519660, +34 1 0 0 0 0 0 0 - XM_044058998.1 5509 1012 1047 NC_056733.1 2000000000 397677551 397677586 1 35, 4462, 397677551, +63 4 0 0 0 0 0 0 - XM_044058998.1 5509 984 1051 NC_056733.1 2000000000 433332509 433332576 1 67, 4458, 433332509, +72 4 0 0 0 0 1 2 - XM_044058998.1 5509 980 1056 NC_056733.1 2000000000 1507791829 1507791907 2 33,43, 4453,4486, 1507791829,1507791864, +68 4 0 0 0 0 0 0 - XM_044058998.1 5509 984 1056 NC_056733.1 2000000000 1655446883 1655446955 1 72, 4453, 1655446883, +58 0 0 0 1 7 2 7 - XM_044058998.1 5509 984 1049 NC_056733.1 2000000000 1939571362 1939571427 3 40,5,13, 4460,4507,4512, 1939571362,1939571406,1939571414, +61 6 0 0 0 0 0 0 - XM_044058998.1 5509 984 1051 NC_056734.1 1017585886 34508101 34508168 1 67, 4458, 34508101, +111 9 0 0 0 0 0 0 - XM_044058998.1 5509 937 1057 NC_056734.1 1017585886 450620563 450620683 1 120, 4452, 450620563, +61 3 0 0 0 0 0 0 - XM_044058998.1 5509 984 1048 NC_056734.1 1017585886 591073842 591073906 1 64, 4461, 591073842, +66 6 0 0 0 0 0 0 - XM_044058998.1 5509 984 1056 NC_056734.1 1017585886 643645705 643645777 1 72, 4453, 643645705, +61 6 0 0 0 0 0 0 - XM_044058998.1 5509 984 1051 NC_056735.1 2000000000 669170310 669170377 1 67, 4458, 669170310, +91 4 0 0 2 6 2 8 - XM_044058998.1 5509 950 1051 NC_056735.1 2000000000 895811671 895811774 3 49,38,8, 4458,4512,4551, 895811671,895811724,895811766, +108 11 0 0 0 0 1 1 - XM_044058998.1 5509 937 1056 NC_056735.1 2000000000 1590515840 1590515960 2 110,9, 4453,4563, 1590515840,1590515951, +60 1 0 0 1 6 2 6 - XM_044058998.1 5509 984 1051 NC_056735.1 2000000000 1684397541 1684397608 3 43,5,13, 4458,4507,4512, 1684397541,1684397587,1684397595, +57 4 0 0 0 0 0 0 - XM_044058998.1 5509 986 1047 NC_056735.1 2000000000 1825238536 1825238597 1 61, 4462, 1825238536, +55 1 0 0 1 11 3 11 - XM_044058998.1 5509 984 1051 NC_056735.1 2000000000 1935782993 1935783060 4 33,5,5,13, 4458,4502,4507,4512, 1935782993,1935783033,1935783039,1935783047, +81 6 0 0 0 0 0 0 - XM_044058998.1 5509 969 1056 NC_056737.1 2000000000 1437919578 1437919665 1 87, 4453, 1437919578, +100 4 0 0 2 12 1 3 - XM_044058998.1 5509 941 1057 NC_056739.1 2000000000 1035068724 1035068831 3 64,33,7, 4452,4517,4561, 1035068724,1035068788,1035068824, +112 8 0 0 0 0 0 0 - XM_044058998.1 5509 937 1057 NC_056739.1 2000000000 1430413639 1430413759 1 120, 4452, 1430413639, +60 1 0 0 1 6 2 6 - XM_044058998.1 5509 984 1051 NC_056739.1 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