61dc7885a5f1001e2bc189501379088f2b53379d galt Mon Feb 23 15:42:36 2026 -0800 fixes things found automated codereview. for bigBedCmdSupport lib moved slAddHead, removed stray debugmsg and fixed comment and added static keyword. fixed bigChainToChain chromFound = FALSE, removed stray test makefile, fixed existing typo "tines", and added a missing space after issing space before optionMultiVal(). refs #37146 diff --git src/utils/wigToBigWig/tests/makefile src/utils/wigToBigWig/tests/makefile index e074a41286c..1dff5b64c5a 100644 --- src/utils/wigToBigWig/tests/makefile +++ src/utils/wigToBigWig/tests/makefile @@ -1,121 +1,121 @@ kentSrc = ../../.. A = ${DESTBINDIR}/wigToBigWig bigWigToWig = ${DESTBINDIR}/bigWigToWig include ../../../inc/common.mk # this can not be run in parallel due to each test removing and reusing output directories .NOTPARALLEL: .NOTPARALLEL: # files names are reused by tests test: test1 test2 test1: outputDir # generate big wigs ${A} input/testFixed.wig input/test.sizes tmp/testFixed.bigWig ${A} input/testVar.wig input/test.sizes tmp/testVar.bigWig ${A} input/testBedGraph.wig input/test.sizes tmp/testBedGraph.bigWig # get unscaled data back out bigWigToBedGraph tmp/testFixed.bigWig output/testFixed.bedGraph bigWigToBedGraph tmp/testVar.bigWig output/testVar.bedGraph bigWigToBedGraph tmp/testBedGraph.bigWig output/testBedGraph.bedGraph # generate summaries on testFixed at lots of resolutions bigWigSummary tmp/testFixed.bigWig chr7 115597761 115598761 1 > output/tf1.sum bigWigSummary tmp/testFixed.bigWig chr7 115597761 115598761 3 > output/tf3.sum bigWigSummary tmp/testFixed.bigWig chr7 115597761 115598761 10 > output/tf10.sum bigWigSummary tmp/testFixed.bigWig chr7 115597761 115598761 30 > output/tf30.sum bigWigSummary tmp/testFixed.bigWig chr7 115597761 115598761 100 > output/tf100.sum bigWigSummary tmp/testFixed.bigWig chr7 115597761 115598761 300 > output/tf300.sum bigWigSummary tmp/testFixed.bigWig chr7 115597761 115598761 1000 > output/tf1000.sum bigWigSummary tmp/testFixed.bigWig chr7 115597761 115598761 3000 > output/tf3000.sum bigWigSummary tmp/testFixed.bigWig chr7 115597761 115598761 10000 > output/tf10000.sum # generate summaries on testVar at 5 resolutions bigWigSummary tmp/testVar.bigWig chrY 81000 91000 1 > output/tv1.sum bigWigSummary tmp/testVar.bigWig chrY 81000 91000 10 > output/tv10.sum bigWigSummary tmp/testVar.bigWig chrY 81000 91000 100 > output/tv100.sum bigWigSummary tmp/testVar.bigWig chrY 81000 91000 1000 > output/tv1000.sum bigWigSummary tmp/testVar.bigWig chrY 81000 91000 10000 > output/tv10000.sum # generate summaries on testBedGraph at 5 resolutions bigWigSummary tmp/testBedGraph.bigWig chr5 131308806 132230652 1 > output/tbg1.sum bigWigSummary tmp/testBedGraph.bigWig chr5 131308806 132230652 10 > output/tbg10.sum bigWigSummary tmp/testBedGraph.bigWig chr5 131308806 132230652 100 > output/tbg100.sum bigWigSummary tmp/testBedGraph.bigWig chr5 131308806 132230652 1000 > output/tbg1000.sum bigWigSummary tmp/testBedGraph.bigWig chr5 131308806 132230652 10000 > output/tbg10000.sum # Do the diff diff output expected ${bigWigToWig} tmp/testFixed.bigWig output/testFixed.wig ${bigWigToWig} tmp/testVar.bigWig output/testVar.wig ${bigWigToWig} tmp/testBedGraph.bigWig output/testBedGraph.wig # note that the text dumps have many small differences that make # it difficult to simply compare input with output, things like - # rounding of floating differneces, one has comments the other lacks, + # rounding of floating differences, one has comments the other lacks, # having rows in different order by chromsome name. # re-generate big wigs from dumped text ${A} output/testFixed.wig input/test.sizes tmp/testFixed.bigWig2 ${A} output/testVar.wig input/test.sizes tmp/testVar.bigWig2 ${A} output/testBedGraph.wig input/test.sizes tmp/testBedGraph.bigWig2 diff tmp/testFixed.bigWig tmp/testFixed.bigWig2 diff tmp/testVar.bigWig tmp/testVar.bigWig2 diff tmp/testBedGraph.bigWig tmp/testBedGraph.bigWig2 # clean up temporary directories rm -r output tmp test2: outputDir mkdir -p tmp output # generate big wigs ${A} -fixedSummaries -keepAllChromosomes input/testFixed.wig input/test.sizes tmp/testFixed.bigWig ${A} -fixedSummaries -keepAllChromosomes input/testVar.wig input/test.sizes tmp/testVar.bigWig ${A} -fixedSummaries -keepAllChromosomes input/testBedGraph.wig input/test.sizes tmp/testBedGraph.bigWig # get unscaled data back out bigWigToBedGraph tmp/testFixed.bigWig output/testFixed.bedGraph bigWigToBedGraph tmp/testVar.bigWig output/testVar.bedGraph bigWigToBedGraph tmp/testBedGraph.bigWig output/testBedGraph.bedGraph # generate summaries on testFixed at lots of resolutions bigWigSummary tmp/testFixed.bigWig chr7 115597761 115598761 1 > output/tf1.sum bigWigSummary tmp/testFixed.bigWig chr7 115597761 115598761 3 > output/tf3.sum bigWigSummary tmp/testFixed.bigWig chr7 115597761 115598761 10 > output/tf10.sum bigWigSummary tmp/testFixed.bigWig chr7 115597761 115598761 30 > output/tf30.sum bigWigSummary tmp/testFixed.bigWig chr7 115597761 115598761 100 > output/tf100.sum bigWigSummary tmp/testFixed.bigWig chr7 115597761 115598761 300 > output/tf300.sum bigWigSummary tmp/testFixed.bigWig chr7 115597761 115598761 1000 > output/tf1000.sum bigWigSummary tmp/testFixed.bigWig chr7 115597761 115598761 3000 > output/tf3000.sum bigWigSummary tmp/testFixed.bigWig chr7 115597761 115598761 10000 > output/tf10000.sum # generate summaries on testVar at 5 resolutions bigWigSummary tmp/testVar.bigWig chrY 81000 91000 1 > output/tv1.sum bigWigSummary tmp/testVar.bigWig chrY 81000 91000 10 > output/tv10.sum bigWigSummary tmp/testVar.bigWig chrY 81000 91000 100 > output/tv100.sum bigWigSummary tmp/testVar.bigWig chrY 81000 91000 1000 > output/tv1000.sum bigWigSummary tmp/testVar.bigWig chrY 81000 91000 10000 > output/tv10000.sum # generate summaries on testBedGraph at 5 resolutions bigWigSummary tmp/testBedGraph.bigWig chr5 131308806 132230652 1 > output/tbg1.sum bigWigSummary tmp/testBedGraph.bigWig chr5 131308806 132230652 10 > output/tbg10.sum bigWigSummary tmp/testBedGraph.bigWig chr5 131308806 132230652 100 > output/tbg100.sum bigWigSummary tmp/testBedGraph.bigWig chr5 131308806 132230652 1000 > output/tbg1000.sum bigWigSummary tmp/testBedGraph.bigWig chr5 131308806 132230652 10000 > output/tbg10000.sum # Do the diff diff output expected_2 # clean up temporary directories rm -r output tmp clean:: @rm -rf output @rm -rf tmp outputDir: @${MKDIR} -p output @${MKDIR} -p tmp