474b9ac55dcb8e3c4cc56b00d52bd210b7989038
markd
  Thu Mar 7 22:59:45 2024 -0800
create PSLs for supplementary alignments that correct represent the query alignment.  RM: 33209

diff --git src/utils/bamToPsl/tests/makefile src/utils/bamToPsl/tests/makefile
index 0086963..4982637 100644
--- src/utils/bamToPsl/tests/makefile
+++ src/utils/bamToPsl/tests/makefile
@@ -2,31 +2,31 @@
 include ../../../inc/common.mk
 
 PROG = bamToPsl
 
 test: test1 test2
 
 test1: mkout
 	${PROG} input/chr9.NM_020469.2.blat.bam output/$@.psl
 	diff expected/$@.psl output/$@.psl
 
 # FIXME: pslCheck call is disable as this produces invalid PSLs.
 test2: mkout
 	${PROG} -nohead input/multimap.sam -fasta=output/$@.fa output/$@.psl
 	diff expected/$@.psl output/$@.psl
 	diff expected/$@.fa output/$@.fa
-	#pslCheck -verbose=0 -querySizes=input/multimap.qsizes output/$@.psl
+	pslCheck -verbose=0 -querySizes=input/multimap.qsizes output/$@.psl
 
 mkout:
 	@mkdir -p output
 
 clean:
 	rm -rf output
 
 ##
 # chr9.NM_020469.2.blat.bam:
 #
 # twoBitToFa /gbdb/hg38/hg38.2bit:chr9 hg38.chr9.fa
 # wget -O NM_020469.2.ABO.fa \
 #    "http://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?db=nuccore&dopt=fasta&sendto=on&id=NM_020469.2"
 #
 # blat hg38.chr9.fa NM_020469.2.ABO.fa chr9.NM_020469.2.blat.psl