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/input/C57B6NJ-1504.transMap-cases.psl src/utils/pslMapPostChain/tests/input/C57B6NJ-1504.transMap-cases.psl
new file mode 100644
index 0000000..9e12302
--- /dev/null
+++ src/utils/pslMapPostChain/tests/input/C57B6NJ-1504.transMap-cases.psl
@@ -0,0 +1,51 @@
+# this has overlapping blocks that should not be chained
+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,
+
+# fun with negative strand
+32	7	0	0	0	0	0	0	+	ENSMUST00000138149.1	2384	0	39	chr1	198981894	29581098	29581137	1	39,	0,	29581098,
+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,
+6	0	0	0	0	0	0	0	-	ENSMUST00000138149.1	2384	260	266	chrX	175135820	74580071	74580077	1	6,	2118,	74580071,
+489	17	0	45	1	212	2	94	-	ENSMUST00000138149.1	2384	1431	2194	chrX	175135820	74614492	74615137	4	175,119,194,63,	190,577,696,890,	74614492,74614667,74614787,74615074,
+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,
+335	10	0	20	3	1055	5	9157	+	ENSMUST00000138149.1	2384	0	1420	chrX	175135820	76423487	76433009	6	39,122,70,16,96,22,	0,39,161,459,1186,1398,	76423487,76426024,76426600,76429352,76430168,76432987,
+37	1	0	0	0	0	0	0	-	ENSMUST00000138149.1	2384	1	39	chrX	175135820	76437887	76437925	1	38,	2345,	76437887,
+955	40	0	8	5	30	3	6	-	ENSMUST00000138149.1	2384	266	1299	chrX	175135820	76442969	76443978	8	113,136,368,109,15,7,18,237,	1085,1199,1349,1718,1827,1846,1853,1881,	76442969,76443083,76443219,76443587,76443698,76443713,76443723,76443741,
+122	0	0	0	0	0	0	0	+	ENSMUST00000138149.1	2384	39	161	chrX	175135820	76447734	76447856	1	122,	39,	76447734,
+429	136	0	69	8	434	10	16694	+	ENSMUST00000138149.1	2384	231	1299	chrX	175135820	76448683	76466011	15	35,22,27,7,32,5,17,21,83,54,99,51,77,40,64,	231,450,530,557,568,600,615,786,807,890,958,1058,1109,1186,1235,	76448683,76464273,76464746,76464774,76464781,76464826,76464831,76465025,76465048,76465132,76465671,76465770,76465829,76465907,76465947,
+
+# block out of the middle of an exon
+1306	0	0	0	1	119	2	1957	-	ENSMUST00000084922.5	1425	0	1425	chr9	126537099	112819219	112822482	3	724,415,167,	0,843,1258,	112819219,112820062,112822315,
+118	1	0	0	0	0	0	0	-	ENSMUST00000084922.5	1425	582	701	chr9	126537099	112819943	112820062	1	119,	724,	112819943,
+
+# hand-crafted split of psl into three pieces.  Original is:
+# 3398	0	236	0	0	0	2	469209	-	ENSMUST00000070533.4	3634	0	3634	chr1	198981894	3253626	3726469	3	2487,200,947,	0,2487,2687,	3253626,3469258,3725522,
+2487	0	0	0	0	0	0	0	-	ENSMUST00000070533.4	3634	1147	3634	chr1	198981894	3253626	3256113	1	2487,	0,	3253626,
+200	0	0	0	0	0	0	0	-	ENSMUST00000070533.4	3634	947	1147	chr1	198981894	3469258	3469458	1	200,	2487,	3469258,
+947	0	0	0	0	0	0	0	-	ENSMUST00000070533.4	3634	0	947	chr1	198981894	3725522	3726469	1	947,	2687,	3725522,
+
+
+# caused a core dump expanding arrays
+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,
+7	12	45	0	0	0	0	0	+	ENSMUST00000113879.3	981	0	64	chr17	96961345	36188899	36188963	1	64,	0,	36188899,
+0	35	235	0	0	0	0	0	+	ENSMUST00000113879.3	981	64	334	chr17	96961345	36189155	36189425	1	270,	64,	36189155,
+0	24	197	0	0	0	0	0	+	ENSMUST00000113879.3	981	334	555	chr17	96961345	36189615	36189836	1	221,	334,	36189615,
+0	9	39	0	0	0	0	0	+	ENSMUST00000113879.3	981	562	610	chr17	96961345	36189843	36189891	1	48,	562,	36189843,
+36	10	18	0	0	0	0	0	+	ENSMUST00000113879.3	981	0	64	chr17	96961345	36316994	36317058	1	64,	0,	36316994,
+0	38	232	0	0	0	0	0	+	ENSMUST00000113879.3	981	64	334	chr17	96961345	36317254	36317524	1	270,	64,	36317254,
+0	25	196	0	0	0	0	0	+	ENSMUST00000113879.3	981	334	555	chr17	96961345	36317711	36317932	1	221,	334,	36317711,
+0	4	51	0	0	0	0	0	+	ENSMUST00000113879.3	981	555	610	chr17	96961345	36317932	36317987	1	55,	555,	36317932,
+0	2	126	0	0	0	0	0	+	ENSMUST00000113879.3	981	723	851	chr17	96961345	36322079	36322207	1	128,	723,	36322079,
+40	0	90	0	0	0	1	127	+	ENSMUST00000113879.3	981	851	981	chr17	96961345	36322355	36322612	2	35,95,	851,886,	36322355,36322517,
+0	9	86	0	0	0	1	1	+	ENSMUST00000113879.3	981	886	981	chr17	96961345	36338491	36338587	2	62,33,	886,948,	36338491,36338554,
+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,
+0	0	276	0	0	0	0	0	+	ENSMUST00000113879.3	981	334	610	chr17	96961345	36375431	36375707	1	276,	334,	36375431,
+0	90	520	0	0	0	2	376	+	ENSMUST00000113879.3	981	0	610	chr17	96961345	36416539	36417525	3	64,270,276,	0,64,334,	36416539,36416799,36417249,
+18	28	256	46	2	23	2	128	+	ENSMUST00000113879.3	981	610	981	chr17	96961345	36418325	36418801	5	138,128,47,2,33,	610,758,886,946,948,	36418325,36418463,36418718,36418765,36418768,
+
+
+# '3 internal end on exon split in to pieces
+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,