dc808927b55b21c72db0cd528f76624fcba339dd max Mon Jan 24 05:15:33 2022 -0800 adding igv-style chrom alias support to chromToUcsc, refs #28722 diff --git src/utils/chromToUcsc/tests/makefile src/utils/chromToUcsc/tests/makefile index a95bb3f..ac45711 100644 --- src/utils/chromToUcsc/tests/makefile +++ src/utils/chromToUcsc/tests/makefile @@ -1,34 +1,37 @@ kentSrc = ../../.. include ../../../inc/common.mk all: mkdir -p out # alas, our automated tests cannot output anything to stderr, as otherwise emails will be sent rm -f out/test.err python2 ${DESTBINDIR}/chromToUcsc -i in/hg19.bed -o out/hg19.bed -a hg19.chromAlias.tsv 2>> out/test.err python2 ${DESTBINDIR}/chromToUcsc -i in/mm10.bed -o out/mm10.bed -a mm10.chromAlias.tsv 2>> out/test.err 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>> out/test.err python3 ${DESTBINDIR}/chromToUcsc -i in/mm10.bed -o out/mm10.bed -a mm10.chromAlias.tsv 2>> out/test.err 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>> out/test.err diff out/hg19.bed expected/hg19.bed python2 ${DESTBINDIR}/chromToUcsc -i in/hg19.vcf.gz -o out/hg19.vcf -a hg19.chromAlias.tsv 2>> out/test.err 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>> out/test.err diff out/mm10.ebi.sam expected/mm10.ebi.sam python3 ${DESTBINDIR}/chromToUcsc -i in/grc38.100.gtf.gz -a mm10.chromAlias.tsv -o out/mm10.gtf 2>> out/test.err diff out/mm10.gtf expected/mm10.gtf python3 ${DESTBINDIR}/chromToUcsc -i in/grc38.100.gtf.gz -a mm10.chromAlias.tsv -o out/mm10.gtf 2>> out/test.err diff out/mm10.gtf expected/mm10.gtf python3 ${DESTBINDIR}/chromToUcsc -s -i in/mm10.bad-names.bed -a mm10.chromAlias.tsv -o out/mm10.bad-names.bed >& out/mm10.bad-names.err diff expected/mm10.bad-names.err out/mm10.bad-names.err diff expected/mm10.bad-names.bed out/mm10.bad-names.bed + python3 ${DESTBINDIR}/chromToUcsc -s -i in/genark.bed -a GCF_002742125.1.chromAlias.txt -o out/genark.bed >& out/genark.err + diff expected/genark.err out/genark.err + diff expected/genark.bed out/genark.bed test: all clean: rm -f out/*