fdd9aae7db69e2c910f0a2cb0dc1fea0fc00f3cd
angie
  Thu May 31 12:35:34 2018 -0700
New program chainBridge (refs #21651): try to bridge double-sided gaps in chains,
first by trivially extending over perfect matches if possible,
then by banded S-W alignment if gap sizes are similar on t and q and
not too large.  This is useful for fixing up some double-sided gaps
that skip identical or nearly identical sequences found in some of
our liftOver chain files.

In doSameSpeciesLiftOver.pl, pipe axtChain to chainBridge.

diff --git src/hg/mouseStuff/makefile src/hg/mouseStuff/makefile
index 5627d8c..a3765b6 100644
--- src/hg/mouseStuff/makefile
+++ src/hg/mouseStuff/makefile
@@ -1,104 +1,105 @@
 # Build all directories in makeDb 
 
 kentSrc = ../..
 
 include ${kentSrc}/inc/localEnvironment.mk
 include ${kentSrc}/inc/common.mk
 
 BADDIRS = \
         correctEst
 
 # List of directories to build for userApps
 UTILS_APPLIST = \
 	axtChain \
 	axtSort \
 	axtSwap \
 	axtToMaf \
 	axtToPsl \
 	bedCoverage \
 	chainAntiRepeat \
 	chainFilter \
 	chainMergeSort \
 	chainNet \
 	chainPreNet \
 	chainSort \
 	chainSplit \
 	chainStitchId \
 	chainSwap \
 	chainToAxt \
 	chainToPsl \
 	chainToPslBasic \
 	lavToAxt \
 	lavToPsl \
 	mafCoverage \
 	mafFetch \
 	mafRanges \
 	mafToAxt \
 	mafToPsl \
 	netChainSubset \
 	netClass \
 	netFilter \
 	netSplit \
 	netSyntenic \
 	netToAxt \
 	netToBed \
 	pslMrnaCover
 
 # List of directories to build at UCSC
 DIRS = \
 	axtAndBed \
 	axtBest \
 	axtCalcMatrix \
 	axtDropOverlap \
 	axtDropSelf \
 	axtFilter \
 	axtIndex \
 	axtPretty \
 	axtQueryCount \
 	axtRecipBest \
 	axtRescore \
 	axtSplitByTarget \
 	axtToBed \
 	axtToChain \
 	calcGap \
+	chainBridge \
 	chainDbToFile \
 	gcForBed \
 	knownVsBlat \
 	libScan \
 	mousePoster \
 	netStats \
 	netToBedWithId \
         orthologBySynteny \
 	phToPsl \
 	regionPicker \
 	rikenBestInCluster \
 	simpleChain \
 	splitSim \
 	subsetAxt \
 	subsetTraces \
 	whyConserved 
 
 # List of directories to build
 USE_DIRS = $(DIRS) $(UTILS_APPLIST)
 
 all: ${USE_DIRS:%=%.all}
 %.all:
 	cd $* && echo $* && ${MAKE}
 
 userApps: $(UTILS_APPLIST:%=%.userApp)
 %.userApp:
 	cd $* && echo $* && $(MAKE)
 
 clean:: $(USE_DIRS:%=%.cleanAll)
 %.cleanAll:
 	cd $* && echo $* && $(MAKE) clean
 
 clean::
 	cd simpleChain && ${MAKE} clean
 
 testAll: $(USE_DIRS:%=%.testAll)
 
 %.testAll:
 	@test -s $*/tests/makefile && (echo $*; cd $* && $(MAKE) test) || true
 
 test:: testAll