b91a917e39c8d58d0de5e6325606f098ef0fb60b
angie
  Wed Mar 21 09:22:21 2018 -0700
New util pslMismatchGapToBed searches for sequence mismatches and indels between reference genome and transcripts.
Five output BED+ files are created, with corresponding hg/lib/txAli*.as autoSql files for generating bigBed.
This could be used to create 'Anomalies' subtracks for the NCBI RefSeq track.  refs #21079

diff --git src/hg/utils/makefile src/hg/utils/makefile
index 78b3669..849f6a7 100644
--- src/hg/utils/makefile
+++ src/hg/utils/makefile
@@ -60,30 +60,31 @@
 	mergeSortedBed3Plus.pl \
 	${USER_APP_SCRIPTS}
 
 APP_SCRIPTS = ${SCRIPT_FILES}
 
 # List of directories to build of interest only at UCSC
 DIRS = ${buildRefresh} \
 	automation \
 	buildReleaseLog \
 	checkUrlsInTable \
 	geoMirrorNode \
 	hgvsToVcf \
 	makeTrackIndex \
 	mysqlSecurityCheck \
 	pslFixCdsJoinGap \
+	pslMismatchGapToBed \
 	pslUniq \
 	refSeqGet \
 	safePush \
 	toDev64 \
 	vcfToHgvs \
 	wigBedToStep
 
 TEST_DIRS = \
 	genePredFilter \
 	genePredToProt \
 	gff3ToGenePred \
 	gff3ToPsl \
 	gtfToGenePred \
 	hgvsToVcf \
 	hubCheck \