51aef9631658a9ec173d7c5aa8989738ae4a71ba
braney
  Thu Oct 7 17:01:53 2021 -0700
add a fix to a bug where liftOver elements with zero size that did *not*
fit into a chain were flagges as an error rather than just marked as
missing

diff --git src/hg/liftOver/tests/makefile src/hg/liftOver/tests/makefile
index e862075..00a5ca4 100644
--- src/hg/liftOver/tests/makefile
+++ src/hg/liftOver/tests/makefile
@@ -1,28 +1,36 @@
 kentSrc = ../../..
 include ../../../inc/common.mk
 
 # make VERBOSE=-verbose=2 will echo out positions as they convert
 
-test:   bin bedPlus3 bed8 bed12 simpleTest minus enm001 chuckTest chuckBigTest enr223 scaffoldEndBug
+test:   bin bedPlus3 bed8 bed12 simpleTest minus enm001 chuckTest chuckBigTest enr223 scaffoldEndBug zeroWidth
 
 # tests too slow to use in default test suite
 testSlow: mm3 multiple
 
 liftOver=${DESTBINDIR}/liftOver
 liftOverMerge=${DESTBINDIR}/liftOverMerge
 
+zeroWidth:	mkdirs
+	${liftOver} \
+            input/zeroWidth.bed \
+            /cluster/data/hg19/bed/liftOver/hg19ToHg38.over.chain.gz \
+                output/zeroWidth.good.bed output/zeroWidth.bad.bed 2> /dev/null
+	cat output/zeroWidth.{good,bad}.bed | \
+                diff - expected/zeroWidth.bed 1>&2
+
 bed12:	mkdirs
 	${liftOver} \
             input/bed12.bed \
             /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