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/hg/utils/pslMap/tests/makefile src/hg/utils/pslMap/tests/makefile
deleted file mode 100644
index 7f90123..0000000
--- src/hg/utils/pslMap/tests/makefile
+++ /dev/null
@@ -1,107 +0,0 @@
-kentSrc = ../../../..
-include ${kentSrc}/inc/common.mk
-
-#pslMap = valgrind --tool=memcheck --num-callers=25 pslMap
-pslMap = ${DESTBINDIR}/pslMap
-pslSwap = ${DESTBINDIR}/pslSwap
-blastToPsl = ${DESTBINDIR}/blastToPsl
-pslCheck = ${DESTBINDIR}/pslCheck
-chainSwap = ${DESTBINDIR}/chainSwap
-
-all:
-
-test:	gapBoth mrnaMrnaMap mrnaMrnaXMap mrnaMapOver mrnaMapOverSwap \
-	mrnaMapOverChain mrnaMapOverChainSwap testMapFileWithInQName
-
-# things with large files that we want to remove their big history from cvs
-# but soon will replace with short versions and no big history.
-# temporarily moved to /hive/users/galt/largeCvsFiles/kent/...
-# input/kgMRna.psl
-# input/negQ.chain
-testnot: kgProt 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.
-# also check mapInfo on unmapped entries
-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
-	${pslMap} -swapMap -mappingPsls=output/$@.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
-	${pslMap} -chainMapFile -mappingPsls=output/$@.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
-
-# -mapFileWithInQName
-testMapFileWithInQName: mkdirs
-	${pslMap} -mapFileWithInQName input/gencode.src.psl input/gencode.blocks.qName-psl output/$@.psl
-	${pslCheck} -verbose=0 output/$@.psl
-	diff -u expected/$@.psl output/$@.psl
-
-clean::
-	rm -rf output
-
-mkdirs:
-	@${MKDIR} output