ad6ef3b792cf6a41a1a01191eee9d73aa68c9504
max
  Tue Jan 26 06:49:35 2021 -0800
update chromToUcsc to work with BAM files, refs #26839

diff --git src/utils/chromToUcsc/tests/makefile src/utils/chromToUcsc/tests/makefile
index 459127a..3debddb 100644
--- src/utils/chromToUcsc/tests/makefile
+++ src/utils/chromToUcsc/tests/makefile
@@ -3,19 +3,22 @@
 
 
 all:
 	mkdir -p out
 	# alas, our automated tests cannot output anything to stderr, as otherwise emails will be sent
 	python2 ${DESTBINDIR}/chromToUcsc -i in/hg19.bed -o out/hg19.bed -a hg19.chromAlias.tsv 2> /dev/null
 	python2 ${DESTBINDIR}/chromToUcsc  -i in/mm10.bed -o out/mm10.bed -a mm10.chromAlias.tsv 2> /dev/null
 	diff out/hg19.bed expected/hg19.bed
 	diff out/mm10.bed expected/mm10.bed
 	python3 ${DESTBINDIR}/chromToUcsc  -i in/hg19.bed -o out/hg19.bed -a hg19.chromAlias.tsv 2> /dev/null
 	python3 ${DESTBINDIR}/chromToUcsc  -i in/mm10.bed -o out/mm10.bed -a mm10.chromAlias.tsv 2> /dev/null
 	diff out/hg19.bed expected/hg19.bed
 	diff out/mm10.bed expected/mm10.bed
 	python3 ${DESTBINDIR}/chromToUcsc  -i in/hg19.bed -o out/hg19.bed -a https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/chromAlias.txt.gz 2> /dev/null
 	diff out/hg19.bed expected/hg19.bed
-	python2 ${DESTBINDIR}/chromToUcsc -i in/hg19.vcf -o out/hg19.vcf -a hg19.chromAlias.tsv 2> /dev/null
+	python2 ${DESTBINDIR}/chromToUcsc -i in/hg19.vcf.gz -o out/hg19.vcf -a hg19.chromAlias.tsv 2> /dev/null
+	diff out/hg19.vcf expected/hg19.vcf
+	python3 ${DESTBINDIR}/chromToUcsc  -i in/mm10.ebi.sam.gz -a mm10.chromAlias.tsv -o out/mm10.ebi.sam 2> /dev/null
+	diff out/mm10.ebi.sam expected/mm10.ebi.sam
 
 clean:
 	rm -f out/*