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/pslMapPostChain/tests/expected/C57B6NJ-1504TransMapTest.psl src/utils/pslMapPostChain/tests/expected/C57B6NJ-1504TransMapTest.psl
new file mode 100644
index 0000000..d3f0f3b
--- /dev/null
+++ src/utils/pslMapPostChain/tests/expected/C57B6NJ-1504TransMapTest.psl
@@ -0,0 +1,21 @@
+2936	0	0	0	1	380	12	24090	+	ENSMUST00000068791.6	3316	0	3316	chr1	198981894	133840173	133867199	14	245,191,84,91,108,215,118,46,104,90,96,121,456,971,	0,245,436,520,611,719,934,1052,1098,1202,1292,1388,1509,2345,	133840173,133841220,133842159,133842624,133845158,133847202,133848077,133850693,133851575,133852292,133853499,133855292,133865772,133866228,
+172	5	0	0	0	0	0	0	+	ENSMUST00000068791.6	3316	2130	2307	chr1	198981894	133866051	133866228	1	177,	2130,	133866051,
+89	3	0	0	0	0	0	0	+	ENSMUST00000068791.6	3316	1965	2057	chr1	198981894	133866228	133866320	1	92,	1965,	133866228,
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+1269	59	0	0	2	1017	6	55809	+	ENSMUST00000138149.1	2384	39	2384	chrX	175135820	76295941	76353078	7	122,153,138,629,96,19,171,	39,266,419,557,1186,2194,2213,	76295941,76298801,76299090,76299229,76299859,76352883,76352907,
+475	10	0	34	3	879	4	36163	+	ENSMUST00000138149.1	2384	0	1398	chrX	175135820	74575694	74612376	6	39,70,221,86,4,99,	0,161,965,1186,1295,1299,	74575694,74578407,74581227,74581449,74581535,74612277,
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+1444	57	0	53	7	374	6	1827932	-	ENSMUST00000138149.1	2384	266	2194	chrX	175135820	74614492	76443978	12	175,119,194,63,113,136,368,109,15,7,18,237,	190,577,696,890,1085,1199,1349,1718,1827,1846,1853,1881,	74614492,74614667,74614787,74615074,76442969,76443083,76443219,76443587,76443698,76443713,76443723,76443741,
+43	1	0	0	1	221	1	1857810	-	ENSMUST00000138149.1	2384	1	266	chrX	175135820	74580071	76437925	2	6,38,	2118,2345,	74580071,76437887,
+3634	0	0	0	0	0	2	469209	-	ENSMUST00000070533.4	3634	0	3634	chr1	198981894	3253626	3726469	3	2487,200,947,	0,2487,2687,	3253626,3469258,3725522,
+18	118	776	46	2	23	5	1304	+	ENSMUST00000113879.3	981	0	981	chr17	96961345	36416539	36418801	8	64,270,276,138,128,47,2,33,	0,64,334,610,758,886,946,948,	36416539,36416799,36417249,36418325,36418463,36418718,36418765,36418768,
+36	48	526	0	0	0	2	58103	+	ENSMUST00000113879.3	981	0	610	chr17	96961345	36316994	36375707	3	64,270,276,	0,64,334,	36316994,36317254,36375431,
+47	78	743	0	1	113	5	132845	+	ENSMUST00000113879.3	981	0	981	chr17	96961345	36188899	36322612	7	64,270,221,55,128,35,95,	0,64,334,555,723,851,886,	36188899,36189155,36317711,36317932,36322079,36322355,36322517,
+0	42	322	0	2	283	3	148608	+	ENSMUST00000113879.3	981	334	981	chr17	96961345	36189615	36338587	4	221,48,62,33,	334,562,886,948,	36189615,36189843,36338491,36338554,
+11	102	497	0	0	0	2	410	-	ENSMUST00000113879.3	981	0	610	chr17	96961345	34860538	34861558	3	276,270,64,	371,647,917,	34860538,34861021,34861494,
+0	85	525	0	0	0	2	377	-	ENSMUST00000113879.3	981	0	610	chr17	96961345	34882952	34883939	3	276,270,64,	371,647,917,	34882952,34883415,34883875,
+31	14	422	5	0	0	2	354	-	ENSMUST00000113879.3	981	0	472	chr17	96961345	36359145	36359971	3	138,270,64,	509,647,917,	36359145,36359470,36359907,
+1424	1	0	0	0	0	1	1838	-	ENSMUST00000084922.5	1425	0	1425	chr9	126537099	112819219	112822482	4	724,119,415,167,	0,724,843,1258,	112819219,112819943,112820062,112822315,
+1434	0	72	0	0	0	11	32636	+	ENSMUST00000187170.2	1506	0	1506	chr1	198981894	66098475	66132617	12	145,188,75,35,101,36,52,120,167,163,122,302,	0,145,333,408,443,544,580,632,752,919,1082,1204,	66098475,66098866,66108617,66109994,66116026,66119066,66120959,66122549,66126111,66129607,66131503,66132315,
+118	0	0	0	0	0	0	0	+	ENSMUST00000187170.2	1506	1082	1200	chr1	198981894	66132197	66132315	1	118,	1082,	66132197,