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/makefile src/utils/pslMap/tests/makefile
index 55c92a7..178d409 100644
--- src/utils/pslMap/tests/makefile
+++ src/utils/pslMap/tests/makefile
@@ -84,24 +84,25 @@
 # would get lost
 negQChain: mkdirs
 	${pslMap} -chainMapFile input/negQ.refSeq.psl input/negQ.chain output/$@.psl
 	${pslCheck} -verbose=0 output/$@.psl
 	diff -u expected/$@.psl output/$@.psl
 
 # retro/parent alignment through mRNA, with -simplifyMappingIds
 retroParent: mkdirs
 	${pslMap} -simplifyMappingIds -swapIn -mapInfo=output/$@.mapinfo input/retro.psl input/parent.psl output/$@.psl
 	${pslCheck} -verbose=0 output/$@.psl
 	diff -u expected/$@.psl output/$@.psl
 	diff -u expected/$@.mapinfo output/$@.mapinfo
 
 # -mapFileWithInQName
 testMapFileWithInQName: mkdirs
-	${pslMap} -mapFileWithInQName input/gencode.src.psl input/gencode.blocks.qName-psl output/$@.psl
+	${pslMap} -mapFileWithInQName -mapInfo=output/$@.mapinfo input/gencode.src.psl input/gencode.blocks.qName-psl output/$@.psl
 	${pslCheck} -verbose=0 output/$@.psl
 	diff -u expected/$@.psl output/$@.psl
+	diff -u expected/$@.mapinfo output/$@.mapinfo
 
 clean::
 	rm -rf output
 
 mkdirs:
 	@${MKDIR} output