da79c37696a46e9978a93218407e6afcdc71326c
galt
  Fri Aug 14 17:45:37 2020 -0700
Fixed bug in hgLiftOver CGI and liftOver utility reported by user. Also tested liftability of knwonGene on Chr1 to panTro6. All remining cases of Boundary error are real and not due to a bug. Added test cases, especially for BED12 which had been oddly missing. refs #26057.

diff --git src/hg/liftOver/tests/makefile src/hg/liftOver/tests/makefile
index 4180f68..e862075 100644
--- src/hg/liftOver/tests/makefile
+++ src/hg/liftOver/tests/makefile
@@ -1,32 +1,32 @@
 kentSrc = ../../..
 include ../../../inc/common.mk
 
 # make VERBOSE=-verbose=2 will echo out positions as they convert
 
-test:   bin bedPlus3 bed8 simpleTest minus enm001 chuckTest chuckBigTest enr223 scaffoldEndBug
+test:   bin bedPlus3 bed8 bed12 simpleTest minus enm001 chuckTest chuckBigTest enr223 scaffoldEndBug
 
 # tests too slow to use in default test suite
 testSlow: mm3 multiple
 
 liftOver=${DESTBINDIR}/liftOver
 liftOverMerge=${DESTBINDIR}/liftOverMerge
 
 bed12:	mkdirs
-	${liftOver} -hasBin -bedPlus=12 \
+	${liftOver} \
             input/bed12.bed \
-            /cluster/data/hg16/bed/liftOver/hg16ToHg17.over.chain \
+            /cluster/data/hg38/bed/liftOver/hg38ToPanTro6.over.chain.gz \
                 output/bed12.good.bed output/bed12.bad.bed 2> /dev/null
 	cat output/bed12.{good,bad}.bed | \
                 diff - expected/bed12.bed 1>&2
 
 bed8:	mkdirs
 	${liftOver} \
             input/bed8.bed \
             /cluster/data/hg16/bed/liftOver/hg16ToHg17.over.chain.gz \
                 output/bed8.good.bed output/bed8.bad.bed 2> /dev/null
 	cat output/bed8.{good,bad}.bed | \
                 diff - expected/bed8.bed 1>&2
 
 bin:    mkdirs
 	${liftOver} -hasBin -bedPlus=6\
             input/bin.bed \