2c3bfb6253d13a518eb2f3697d62224bdfa4aa54
markd
  Thu Mar 7 21:01:21 2024 -0800
add new test cases that shows that bamToPsl is broken; restructure tests to match the rest

diff --git src/utils/bamToPsl/tests/makefile src/utils/bamToPsl/tests/makefile
index 58bc46f..8c6f016 100644
--- src/utils/bamToPsl/tests/makefile
+++ src/utils/bamToPsl/tests/makefile
@@ -1,23 +1,39 @@
 kentSrc = ../../..
 include ../../../inc/common.mk
 
 PROG = bamToPsl
 
-test:
-	${PROG} chr9.NM_020469.2.blat.bam testOut.psl
-	@diff expectedOut.psl testOut.psl
-	${MAKE} clean
+test: test1 test2
 
-clean:
-	rm -f testOut.psl
+test1: mkout
+	${PROG} input/chr9.NM_020469.2.blat.bam output/$@.psl
+	diff expected/$@.psl output/$@.psl
+
+test2: mkout
+	${PROG} -nohead input/multimap.sam output/$@.psl
+	diff expected/$@.psl output/$@.psl
+	pslCheck -verbose=0 -querySizes=input/multimap.qsizes output/$@.psl
+
+mkout:
+	@mkdir -p output
 
-# the bam file was constructed:
+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
+#