fc825ca18eeb99e3807a73d23fd26b614807fa0f
markd
  Tue Oct 11 19:26:06 2022 -0700
add row number of output psl to pslMap mapInfo file to make it easy to sync up the two files

diff --git src/utils/pslMap/tests/expected/testMapFileWithInQName.mapinfo src/utils/pslMap/tests/expected/testMapFileWithInQName.mapinfo
new file mode 100644
index 0000000..433ebda
--- /dev/null
+++ src/utils/pslMap/tests/expected/testMapFileWithInQName.mapinfo
@@ -0,0 +1,18 @@
+#srcQName	srcQStart	srcQEnd	srcQSize	srcTName	srcTStart	srcTEnd	srcStrand	srcAligned	mappingQName	mappingQStart	mappingQEnd	mappingTName	mappingTStart	mappingTEnd	mappingStrand	mappingId	mappedQName	mappedQStart	mappedQEnd	mappedTName	mappedTStart	mappedTEnd	mappedStrand	mappedAligned	qStartTrunc	qEndTrunc	mappedPslLine
+ENSMUST00000145003.1	0	1424	1424	12	57230445	57457232	+	1424	12	57230445	57230611	scaffold-66687	103520	103686	+-	0	ENSMUST00000145003.1	0	166	scaffold-66687	103520	103686	-	166	0	1258	0
+ENSMUST00000145003.1	0	1424	1424	12	57230445	57457232	+	1424	12	57303344	57307464	scaffold-153183	14455	18703	+-	1	ENSMUST00000145003.1	166	606	scaffold-153183	14455	18703	-	440	166	818	1
+ENSMUST00000145003.1	0	1424	1424	12	57230445	57457232	+	1424	12	57325523	57414410	scaffold-290469	11498	103628	+-	2	ENSMUST00000145003.1	606	1144	scaffold-290469	11498	103628	-	538	606	280	2
+ENSMUST00000145003.1	0	1424	1424	12	57230445	57457232	+	1424	12	57456952	57457232	scaffold-100687	127380	127660	+-	3	ENSMUST00000145003.1	1144	1424	scaffold-100687	127380	127660	-	280	1144	0	3
+ENSMUST00000123498.1	0	2117	2117	12	57230445	57497199	+	2117	12	57230445	57230611	scaffold-66687	103520	103686	+-	4	ENSMUST00000123498.1	0	166	scaffold-66687	103520	103686	-	166	0	1951	4
+ENSMUST00000123498.1	0	2117	2117	12	57230445	57497199	+	2117	12	57303344	57307464	scaffold-153183	14455	18703	+-	5	ENSMUST00000123498.1	166	606	scaffold-153183	14455	18703	-	440	166	1511	5
+ENSMUST00000123498.1	0	2117	2117	12	57230445	57497199	+	2117	12	57325523	57414410	scaffold-290469	11498	103628	+-	6	ENSMUST00000123498.1	606	1144	scaffold-290469	11498	103628	-	538	606	973	6
+ENSMUST00000123498.1	0	2117	2117	12	57230445	57497199	+	2117	12	57456952	57457183	scaffold-100687	127429	127660	+-	7	ENSMUST00000123498.1	1144	1375	scaffold-100687	127429	127660	-	231	1144	742	7
+ENSMUST00000123498.1	0	2117	2117	12	57230445	57497199	+	2117	12	57496457	57497199	scaffold-225031	91009	91751	++	8	ENSMUST00000123498.1	1375	2117	scaffold-225031	91009	91751	+	742	1375	0	8
+ENSMUST00000153137.1	0	2158	2158	12	57282172	57467041	+	2158	12	57282172	57307464	scaffold-153183	14455	39826	+-	9	ENSMUST00000153137.1	0	660	scaffold-153183	14455	39826	-	660	0	1498	9
+ENSMUST00000153137.1	0	2158	2158	12	57282172	57467041	+	2158	12	57325523	57414410	scaffold-290469	11498	103628	+-	10	ENSMUST00000153137.1	660	1198	scaffold-290469	11498	103628	-	538	660	960	10
+ENSMUST00000153137.1	0	2158	2158	12	57282172	57467041	+	2158	12	57456952	57467041	scaffold-100687	117557	127660	+-	11	ENSMUST00000153137.1	1198	2158	scaffold-100687	117557	127660	-	960	1198	0	11
+ENSMUST00000130447.1	0	2171	2171	12	57282172	57497199	+	2171	12	57282172	57307464	scaffold-153183	14455	39826	+-	12	ENSMUST00000130447.1	0	660	scaffold-153183	14455	39826	-	660	0	1511	12
+ENSMUST00000130447.1	0	2171	2171	12	57282172	57497199	+	2171	12	57325523	57414410	scaffold-290469	11498	103628	+-	13	ENSMUST00000130447.1	660	1198	scaffold-290469	11498	103628	-	538	660	973	13
+ENSMUST00000130447.1	0	2171	2171	12	57282172	57497199	+	2171	12	57456952	57457183	scaffold-100687	127429	127660	+-	14	ENSMUST00000130447.1	1198	1429	scaffold-100687	127429	127660	-	231	1198	742	14
+ENSMUST00000130447.1	0	2171	2171	12	57282172	57497199	+	2171	12	57496457	57497199	scaffold-225031	91009	91751	++	15	ENSMUST00000130447.1	1429	2171	scaffold-225031	91009	91751	+	742	1429	0	15
+ENSMUST00000128945.1	0	283	283	12	57332428	57366593	+	283	12	57332428	57366593	scaffold-290469	59199	96728	+-	16	ENSMUST00000128945.1	0	283	scaffold-290469	59199	96728	-	283	0	0	16