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
@@ -49,30 +49,31 @@
 	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 \