8fdef9e866ecc228bfe4ea54102d0079818f0366 braney Fri Apr 8 14:49:38 2022 -0700 let bedGraphToBigWig use chromAlias.bb as chromSizes file. Add tests to both bedGraphToBigWig and bedToBigBed diff --git src/utils/bedToBigBed/tests/makefile src/utils/bedToBigBed/tests/makefile index a2b89ab..2384bc4 100644 --- src/utils/bedToBigBed/tests/makefile +++ src/utils/bedToBigBed/tests/makefile @@ -1,57 +1,73 @@ kentSrc = ../../.. A = bedToBigBed include ../../../inc/common.mk -test: testRgb testNotSorted testMultiInsAtEnd itemsRgb tabSep +test: testRgb testNotSorted testMultiInsAtEnd itemsRgb tabSep testBadChrom1 testBbSize1 testBbSize2 + +testBadChrom1: outputDir + -${BINDIR}/${A} input/colored.genbank.bed input/human.chrom.sizes.txt output/noFile.chromAlias.bb -tab -type=bed12+13 -as=input/bigGenePred.as 2> output/testBadChrom1.err + diff expected/testBadChrom1.err output/testBadChrom1.err + +output/human.chromAlias.bb: outputDir + ${BINDIR}/${A} input/human.chromAlias.bed input/human.chrom.sizes.txt output/human.chromAlias.bb -tab -type=bed3+4 -as=input/chromAliasIndex.as -extraIndex=genbank,ensembl,ncbi,ucsc + +testBbSize1: outputDir output/human.chromAlias.bb + ${BINDIR}/${A} input/colored.genbank.bed output/human.chromAlias.bb output/colored.genbank.bb -sizesIsBb -tab -type=bed12+13 -as=input/bigGenePred.as + bigBedToBed output/colored.genbank.bb output/colored.genbank.bed + diff input/colored.genbank.bed output/colored.genbank.bed + +testBbSize2: outputDir output/human.chromAlias.bb + -${BINDIR}/${A} input/mixed.bed output/human.chromAlias.bb output/noFile.chromAlias.bb -sizesIsBb -tab -type=bed12+13 -as=input/bigGenePred.as 2> output/mixed.err + diff expected/mixed.err output/mixed.err testRgb: outputDir ${BINDIR}/${A} -type=bed9 -as=input/itemRgb.as input/itemRgb.bed input/chrom.sizes output/itemRgb.bb 2> /dev/null bigBedToBed output/itemRgb.bb output/test_itemRgb.bed diff input/itemRgb.bed output/test_itemRgb.bed testNotSorted: outputDir -${BINDIR}/${A} -type=bed12 input/notSorted.bed input/notSorted.chrom.sizes /dev/null 2> output/notSorted.err || true diff expected/notSorted.err output/notSorted.err testMultiInsAtEnd: outputDir ${BINDIR}/${A} input/multiInsAtEnd.bed input/chrom.sizes output/multiInsAtEnd.bb 2> /dev/null bigBedToBed output/multiInsAtEnd.bb output/test_multiInsAtEnd.bed diff -w input/multiInsAtEnd.bed output/test_multiInsAtEnd.bed itemsRgb: outputDir ${BINDIR}/${A} input/reservedBed12.bed input/chrom.sizes output/reservedBed12.bb 2> /dev/null bigBedToBed output/reservedBed12.bb output/test_reservedBed12.bed diff input/reservedBed12.bed output/test_reservedBed12.bed ${BINDIR}/${A} -type=bed12 input/reservedBed12.bed input/chrom.sizes output/reservedBed12.bb 2> /dev/null bigBedToBed output/reservedBed12.bb output/test_reservedBed12.bed diff input/reservedBed12.bed output/test_reservedBed12.bed ${BINDIR}/${A} -type=bed9+ -as=input/reservedBed12.as input/reservedBed12.bed input/chrom.sizes output/reservedBed12.bb 2> /dev/null bigBedToBed output/reservedBed12.bb output/test_reservedBed12.bed diff input/reservedBed12.bed output/test_reservedBed12.bed ${BINDIR}/${A} -type=bed9+ -as=input/itemRgbBed12.as input/reservedBed12.bed input/chrom.sizes output/reservedBed12.bb 2> /dev/null bigBedToBed output/reservedBed12.bb output/test_reservedBed12.bed diff input/reservedBed12.bed output/test_reservedBed12.bed ${BINDIR}/${A} input/itemRgbBed12.bed input/chrom.sizes output/itemRgbBed12.bb 2> /dev/null bigBedToBed output/itemRgbBed12.bb output/test_itemRgbBed12.bed diff input/itemRgbBed12.bed output/test_itemRgbBed12.bed ${BINDIR}/${A} -type=bed12 input/itemRgbBed12.bed input/chrom.sizes output/itemRgbBed12.bb 2> /dev/null bigBedToBed output/itemRgbBed12.bb output/test_itemRgbBed12.bed diff input/itemRgbBed12.bed output/test_itemRgbBed12.bed ${BINDIR}/${A} -type=bed12 -as=input/reservedBed12.as input/itemRgbBed12.bed input/chrom.sizes output/itemRgbBed12.bb 2> /dev/null bigBedToBed output/itemRgbBed12.bb output/test_itemRgbBed12.bed diff input/itemRgbBed12.bed output/test_itemRgbBed12.bed ${BINDIR}/${A} -type=bed12 -as=input/itemRgbBed12.as input/itemRgbBed12.bed input/chrom.sizes output/itemRgbBed12.bb 2> /dev/null bigBedToBed output/itemRgbBed12.bb output/test_itemRgbBed12.bed diff input/itemRgbBed12.bed output/test_itemRgbBed12.bed tabSep: outputDir ${BINDIR}/${A} -tab -type=bed4 -as=input/tabSep.as input/tabSep.bed input/chrom.sizes output/tabSep.bb 2> /dev/null bigBedToBed output/tabSep.bb output/test_tabSep.bed diff input/tabSep.bed output/test_tabSep.bed clean:: @rm -rf output outputDir: @${MKDIR} -p output