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/pslMap/tests/input/gencode.blocks.qName-psl src/utils/pslMap/tests/input/gencode.blocks.qName-psl new file mode 100644 index 0000000..71d88ff --- /dev/null +++ src/utils/pslMap/tests/input/gencode.blocks.qName-psl @@ -0,0 +1,17 @@ +ENSMUST00000145003.1 166 0 0 0 0 0 0 0 +- 12 120129022 57230445 57230611 scaffold-66687 460899 103520 103686 1 166, 57230445, 357213, +ENSMUST00000145003.1 438 2 0 0 2 3680 2 3808 +- 12 120129022 57303344 57307464 scaffold-153183 66466 14455 18703 3 207,127,106, 57303344,57306010,57307358, 47763,50559,51905, +ENSMUST00000145003.1 535 3 0 0 4 88349 4 91592 +- 12 120129022 57325523 57414410 scaffold-290469 110530 11498 103628 5 130,34,171,108,95, 57325523,57331995,57332288,57364126,57414315, 6902,13369,13662,48952,98937, +ENSMUST00000145003.1 279 1 0 2 0 0 0 0 +- 12 120129022 57456952 57457232 scaffold-100687 188060 127380 127660 1 280, 57456952, 60400, +ENSMUST00000123498.1 166 0 0 0 0 0 0 0 +- 12 120129022 57230445 57230611 scaffold-66687 460899 103520 103686 1 166, 57230445, 357213, +ENSMUST00000123498.1 438 2 0 0 2 3680 2 3808 +- 12 120129022 57303344 57307464 scaffold-153183 66466 14455 18703 3 207,127,106, 57303344,57306010,57307358, 47763,50559,51905, +ENSMUST00000123498.1 535 3 0 0 4 88349 4 91592 +- 12 120129022 57325523 57414410 scaffold-290469 110530 11498 103628 5 130,34,171,108,95, 57325523,57331995,57332288,57364126,57414315, 6902,13369,13662,48952,98937, +ENSMUST00000123498.1 231 0 0 0 0 0 0 0 +- 12 120129022 57456952 57457183 scaffold-100687 188060 127429 127660 1 231, 57456952, 60400, +ENSMUST00000123498.1 741 1 0 0 0 0 0 0 ++ 12 120129022 57496457 57497199 scaffold-225031 201486 91009 91751 1 742, 57496457, 91009, +ENSMUST00000153137.1 658 2 0 0 4 24632 4 24711 +- 12 120129022 57282172 57307464 scaffold-153183 66466 14455 39826 5 138,82,207,127,106, 57282172,57282873,57303344,57306010,57307358, 26640,27341,47763,50559,51905, +ENSMUST00000153137.1 535 3 0 0 4 88349 4 91592 +- 12 120129022 57325523 57414410 scaffold-290469 110530 11498 103628 5 130,34,171,108,95, 57325523,57331995,57332288,57364126,57414315, 6902,13369,13662,48952,98937, +ENSMUST00000153137.1 959 1 0 0 2 9129 2 9143 +- 12 120129022 57456952 57467041 scaffold-100687 188060 117557 127660 3 231,143,586, 57456952,57460841,57466455, 60400,64287,69917, +ENSMUST00000130447.1 658 2 0 0 4 24632 4 24711 +- 12 120129022 57282172 57307464 scaffold-153183 66466 14455 39826 5 138,82,207,127,106, 57282172,57282873,57303344,57306010,57307358, 26640,27341,47763,50559,51905, +ENSMUST00000130447.1 535 3 0 0 4 88349 4 91592 +- 12 120129022 57325523 57414410 scaffold-290469 110530 11498 103628 5 130,34,171,108,95, 57325523,57331995,57332288,57364126,57414315, 6902,13369,13662,48952,98937, +ENSMUST00000130447.1 231 0 0 0 0 0 0 0 +- 12 120129022 57456952 57457183 scaffold-100687 188060 127429 127660 1 231, 57456952, 60400, +ENSMUST00000130447.1 741 1 0 0 0 0 0 0 ++ 12 120129022 57496457 57497199 scaffold-225031 201486 91009 91751 1 742, 57496457, 91009, +ENSMUST00000128945.1 283 0 0 0 2 33882 2 37246 +- 12 120129022 57332428 57366593 scaffold-290469 110530 59199 96728 3 31,108,144, 57332428,57364126,57366449, 13802,48952,51187,