02336754147822f5aa61ba13277123b2cc629001 markd Thu May 20 08:38:55 2021 -0700 Moved pslMap, pslMapPostChain, pslRc, pslSwap to src/utils, as they do not have hg/lib dependencies. diff --git src/utils/pslSwap/tests/expected/transTest.psl src/utils/pslSwap/tests/expected/transTest.psl new file mode 100644 index 0000000..b99d9d2 --- /dev/null +++ src/utils/pslSwap/tests/expected/transTest.psl @@ -0,0 +1,12 @@ +652 257 0 0 2 16618 0 0 ++ chr1 245522847 42314 59841 NM_001000613 936 0 909 3 162,701,46, 42314,52973,59795, 0,162,863, +749 166 0 0 0 0 0 0 ++ chr1 245522847 52799 53714 NM_146400 966 15 930 1 915, 52799, 15, +771 167 0 0 0 0 0 0 ++ chr1 245522847 52812 53750 NM_001000369 939 1 939 1 938, 52812, 1, +500 154 0 0 5 6805 2 504 -+ chr1 245522847 92653606 92661065 NM_001020776 1480 132 1290 6 57,84,30,135,164,184, 152861782,152862321,152864639,152864784,152866513,152869057, 132,339,777,807,942,1106, +760 155 0 0 0 0 0 0 -+ chr1 245522847 660982 661897 NM_001000579 939 0 915 1 915, 244860950, 0, +760 155 0 0 0 0 0 0 -+ chr1 245522847 660982 661897 NM_001000608 939 0 915 1 915, 244860950, 0, +375 67 0 0 4 1810 3 201 -+ chr1 245522847 4558 6810 AK004209 954 0 643 6 87,50,109,72,17,107, 245516037,245517030,245517080,245517946,245518158,245518182, 0,274,325,434,506,536, +1053 181 0 0 10 8963 3 200 -+ chr1 245522847 4558 14755 AK033616 1764 80 1514 12 155,112,147,141,69,60,195,50,109,72,17,107, 245508092,245514605,245514923,245515242,245515620,245515692,245515929,245517030,245517080,245517946,245518158,245518182, 80,235,347,494,635,704,764,1145,1196,1305,1377,1407, +1057 183 0 0 10 8963 3 200 -+ chr1 245522847 4558 14761 AJ304796 1808 29 1469 12 161,112,147,141,69,60,195,49,110,72,17,107, 245508086,245514605,245514923,245515242,245515620,245515692,245515929,245517030,245517079,245517946,245518158,245518182, 29,190,302,449,590,659,719,1100,1150,1260,1332,1362, +41 10 0 0 0 0 0 0 +- chr1 245522847 2866 2917 AA542579 418 367 418 1 51, 2866, 0, +401 62 0 0 4 6780 1 44 +- chr1 245522847 7488 14731 AA388728 507 0 507 5 117,147,69,40,90, 7488,7777,8130,14600,14641, 0,117,264,377,417, +344 55 0 0 3 6768 1 31 +- chr1 245522847 7576 14743 AA866967 449 15 445 4 29,147,79,144, 7576,7777,8130,14599, 4,33,180,290,