9cf7baf4bc2d17ad036d295fd96f137235915775
markd
  Fri Mar 15 10:57:07 2024 -0700
removed stale FIXME

diff --git src/utils/bamToPsl/tests/makefile src/utils/bamToPsl/tests/makefile
index 4982637..724174a 100644
--- src/utils/bamToPsl/tests/makefile
+++ src/utils/bamToPsl/tests/makefile
@@ -1,41 +1,40 @@
 kentSrc = ../../..
 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
 
 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
 # pslToBed chr9.NM_020469.2.blat.psl chr9.NM_020469.2.blat.bed
 # /cluster/bin/bedtools/bedtools bedtobam -bed12 -i chr9.NM_020469.2.blat.bed \
 #    -g /hive/data/genomes/hg38/chrom.sizes > chr9.NM_020469.2.blat.bam
 
 ##
 # multimap.sam
 # came from mimimap2 aligns of mRNA CAT transcript on hs1 to a
 # Shasta ONT assembly
 #