2d6c8b5aa593976bc312cb3111d9d4cd7b46938a
jcasper
  Wed Oct 2 09:29:18 2024 -0700
Position liftovers need to clean up temp files when they're done, refs #28023

diff --git src/hg/liftOver/tests/makefile src/hg/liftOver/tests/makefile
index 22d8b6a..815281f 100644
--- src/hg/liftOver/tests/makefile
+++ src/hg/liftOver/tests/makefile
@@ -1,24 +1,23 @@
 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 zeroWidth \
 	bed12PreserveInput bed3PreserveInput gffPreserveInput pslPreserveInput samplePreserveInput \
-	genePredPreserveInput gtfPreserveInput
-# omitting positionPreserveInput right now because it creates extra junk files in the current directory
+	genePredPreserveInput gtfPreserveInput positionPreserveInput
 
 # tests too slow to use in default test suite
 testSlow: mm3 multiple
 
 liftOver=${DESTBINDIR}/liftOver
 liftOverMerge=${DESTBINDIR}/liftOverMerge
 # use local binaries if available
 ifneq ($(wildcard ../liftOver),)
   liftOver=../liftOver
 endif
 ifneq ($(wildcard ../liftOverMerge),)
   liftOverMerge=../liftOverMerge
 endif
 
 
@@ -227,30 +226,28 @@
 	${liftOver} -preserveInput -gff \
             input/gffPreserve.gff \
              https://hgdownload.soe.ucsc.edu/admin/exe/testFiles/liftOver/hg38ToPanTro6.over.chain.gz \
                 output/gffPreserve.good.gff output/gffPreserve.bad.gff 2> /dev/null
 	cat output/gffPreserve.{good,bad}.gff | \
                 diff - expected/gffPreserve.gff 1>&2
 
 samplePreserveInput: mkdirs
 	${liftOver} -preserveInput -sample \
             input/samplePreserve.sample \
              https://hgdownload.soe.ucsc.edu/admin/exe/testFiles/liftOver/hg38ToPanTro6.over.chain.gz \
                 output/samplePreserve.good.sample output/samplePreserve.bad.sample 2> /dev/null
 	cat output/samplePreserve.{good,bad}.sample | \
                 diff - expected/samplePreserve.sample 1>&2
 
-# this isn't being tested right now because liftOver -positions creates temp bed files in the current
-# directory and then never cleans them up
 positionPreserveInput: mkdirs
 	${liftOver} -preserveInput -positions \
             input/positionPreserve.pos \
              https://hgdownload.soe.ucsc.edu/admin/exe/testFiles/liftOver/hg38ToPanTro6.over.chain.gz \
                 output/positionPreserve.good.pos output/positionPreserve.bad.pos 2> /dev/null
 	cat output/positionPreserve.{good,bad}.pos | \
                 diff - expected/positionPreserve.pos 1>&2
 
 mkdirs:
 	mkdir -p output
 
 clean:
 	rm -fr output