e4f7eda5f5bb015ddc38f592869339263909854a braney Thu Feb 20 10:03:46 2025 -0800 tweak bedToBigBed to come up with its own temp file name diff --git src/utils/bedToBigBed/tests/makefile src/utils/bedToBigBed/tests/makefile index 895cb6cce6b..50e1729a3a1 100644 --- src/utils/bedToBigBed/tests/makefile +++ src/utils/bedToBigBed/tests/makefile @@ -28,31 +28,31 @@ testCompress: outputDir ${BINDIR}/${A} -type=bed9 -as=input/itemRgb.as input/itemRgb.bed.gz input/chrom.sizes output/itemRgbGz.bb 2> /dev/null bigBedToBed output/itemRgbGz.bb output/test_itemRgbGz.bed diff input/itemRgb.bed output/test_itemRgbGz.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 testSortNotSorted: outputDir - -${BINDIR}/${A} -tab -type=bed9+3 -sort=${TMPDIR}/notSorted.bed input/notSorted.bed input/notSorted.chrom.sizes output/notSorted.bb + -${BINDIR}/${A} -tab -type=bed9+3 -sort input/notSorted.bed input/notSorted.chrom.sizes output/notSorted.bb bigBedToBed output/notSorted.bb output/notSorted.bed diff expected/notSorted.bed output/notSorted.bed testNotSorted: outputDir -${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