b5975d804a51167f783805828c78f811a3ef096b braney Mon Oct 2 14:45:30 2023 -0700 some new tests for relaxed sorting diff --git src/utils/bedToBigBed/tests/makefile src/utils/bedToBigBed/tests/makefile index b033fea..e6ad09e 100644 --- src/utils/bedToBigBed/tests/makefile +++ src/utils/bedToBigBed/tests/makefile @@ -1,47 +1,56 @@ kentSrc = ../../.. A = bedToBigBed include ../../../inc/common.mk -test: testRgb testMultiInsAtEnd itemsRgb tabSep testBadChrom1 testBbSize1 testBbSize2 testDevStdin testStdin testCompress +test: testOddSorted testRgb testMultiInsAtEnd itemsRgb tabSep testBadChrom1 testBbSize1 testBbSize2 testDevStdin testStdin testCompress testNotSorted 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 -sizesIsChromAliasBb -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 -sizesIsChromAliasBb -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 testCompress: outputDir ${BINDIR}/${A} -type=bed9 -as=input/itemRgb.as input/itemRgb.bed.gz 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 +testOddSorted: outputDir + -${BINDIR}/${A} -extraIndex=name -type=bed12+16 -tab -as=../../..//hg/lib/gencodeBGP.as input/oddSorted.bed input/hg38.chrom.sizes output/oddSorted.bb + bigBedToBed output/oddSorted.bb output/oddSorted.bed + LC_ALL=C sort -k1,1 -k2,2n input/oddSorted.bed > output/oddSorted.check.bed + diff output/oddSorted.check.bed output/oddSorted.bed + cut -f 4 input/oddSorted.bed > output/oddSorted.names + bigBedNamedItems output/oddSorted.bb output/oddSorted.names -nameFile stdout | LC_ALL=C sort -k1,1 -k2,2n > output/searchNames.bed + diff output/oddSorted.bed output/searchNames.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