src/hg/pslMap/tests/makefile 1.11

Index: src/hg/pslMap/tests/makefile
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/pslMap/tests/makefile,v
retrieving revision 1.10
retrieving revision 1.11
diff -b -B -U 1000000 -r1.10 -r1.11
--- src/hg/pslMap/tests/makefile	27 Jul 2007 05:26:19 -0000	1.10
+++ src/hg/pslMap/tests/makefile	10 Jul 2009 18:11:56 -0000	1.11
@@ -1,84 +1,88 @@
 include ../../../inc/common.mk
 pslMap = ../pslMap
 #pslMap = valgrind --tool=memcheck --num-callers=25 ../pslMap
 
 all:
 
 test:	kgProt gapBoth mrnaMrnaMap mrnaMrnaXMap mrnaMapOver mrnaMapOverSwap \
 	mrnaMapOverChain mrnaMapOverChainSwap negQChain
 
 
 # basic tests of protein -> mrna -> genome mapping
 kgProt: mkdirs
 	blastToPsl input/kgProtMRna.blast output/kgProtMRna.psl
 	${pslMap} output/kgProtMRna.psl input/kgMRna.psl output/$@.psl
 	pslCheck -verbose=0 output/$@.psl
 	diff -u expected/$@.psl output/$@.psl
 
 # this generated a gap in both query and target
 gapBoth: mkdirs
 	blastToPsl input/gapBothProtMRna.blast output/gapBothProtMRna.psl
 	${pslMap} output/gapBothProtMRna.psl input/gapBothMRna.psl output/$@.psl
 	pslCheck -verbose=0 output/$@.psl
 	diff -u expected/$@.psl output/$@.psl
 
 # mrna->mrna->genome
 mrnaMrnaMap: mkdirs
 	${pslMap} input/mrnaRefSeq.psl input/refSeqGen.psl output/$@.psl
 	pslCheck -verbose=0 output/$@.psl
 	diff -u expected/$@.psl output/$@.psl
 
 # mrna->mrna->genome, using translated mrna/mrna alignments
 mrnaMrnaXMap: mkdirs
 	${pslMap} input/mrnaRefSeqX.psl input/refSeqGen.psl output/$@.psl
 	pslCheck -verbose=0 output/$@.psl
 	diff -u expected/$@.psl output/$@.psl
 
 # mrna->mm6->hg17, using untranslated mrna->mm6.  At one point this
 # got the strand wrong.
 mrnaMapOver: mkdirs
 	${pslMap} -mapInfo=output/$@.mapinfo input/mrnaToMm6.psl input/mm6ToHg17.psl output/$@.psl
 	pslCheck -verbose=0 output/$@.psl
 	diff -u expected/$@.psl output/$@.psl
 	diff -u expected/$@.mapinfo output/$@.mapinfo
 
 # swapped mapping psl, same result as mrnaMapOver
 mrnaMapOverSwap: mkdirs
 	pslSwap -noRc input/mm6ToHg17.psl output/hg17ToMm6.psl
-	${pslMap} -swapMap -mapInfo=output/$@.mapinfo input/mrnaToMm6.psl output/hg17ToMm6.psl output/$@.psl
+	${pslMap} -swapMap -mappingPsls=output/$@.mapping.psl -mapInfo=output/$@.mapinfo input/mrnaToMm6.psl output/hg17ToMm6.psl output/$@.psl
 	pslCheck -verbose=0 output/$@.psl
+	pslCheck -verbose=0 output/$@.mapping.psl
 	diff -u expected/mrnaMapOver.psl output/$@.psl
 	diff -u expected/$@.mapinfo output/$@.mapinfo
+	diff -u expected/$@.mapping.psl output/$@.mapping.psl
 
 # use chain, same results as mrnaMapOver
 mrnaMapOverChain: mkdirs
-	${pslMap} -chainMapFile input/mrnaToMm6.psl input/mm6ToHg17.chain output/$@.psl
+	${pslMap} -chainMapFile -mappingPsls=output/$@.mapping.psl input/mrnaToMm6.psl input/mm6ToHg17.chain output/$@.psl
 	pslCheck -verbose=0 output/$@.psl
+	pslCheck -verbose=0 output/$@.mapping.psl
 	diff -u expected/mrnaMapOver.psl output/$@.psl
+	diff -u expected/$@.mapping.psl output/$@.mapping.psl
 
 # use chain swapped, same results as mrnaMapOver
 mrnaMapOverChainSwap: mkdirs
 	chainSwap input/mm6ToHg17.chain output/hg17ToMm6.chain 
 	${pslMap} -chainMapFile -swapMap input/mrnaToMm6.psl output/hg17ToMm6.chain output/$@.psl
 	pslCheck -verbose=0 output/$@.psl
 	diff -u expected/mrnaMapOver.psl output/$@.psl
 
 # bug created with binKeeper optimization where negative strand query chains
 # 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
 
 clean::
 	rm -rf output
 
 mkdirs:
 	@${MKDIR} output