d87ef2fb8472135b899fd1a89434033d5895217a mspeir Thu Oct 1 15:31:26 2026 -0700 Add barChartReorder, a utility for changing the order of the bars in a barChart track, refs #37619 The bars of a barChart are drawn in the order their values appear in the expScores field, and nothing re-sorts them when the track is drawn, so the order is a property of the data file. Putting the bars in a different order means rewriting that field in every row, which is awkward enough by hand that we have twice done it for a data author instead of explaining it. This has come up on #36998 and #37001. barChartReorder takes the current bar order and the wanted order as two lists of names, rewrites expScores in every row, optionally puts a .categories file into the same order, and prints the barChartBars line for the track. It works on any barChart BED whatever produced it, so unlike the --groupOrderFile option of expMatrixToBarchartBed it does not assume the file was built here from an expression matrix. A bigBarChart is handled by converting it with bigBedToBed and rebuilding it afterwards, which the usage message spells out. It refuses to write a half-correct file: the two orders must name the same bars, every row must hold as many values as there are names, and a .categories file must have a row for each bar. Listed in USER_APP_SCRIPTS so it reaches hgdownload, and in the no-argument branch of mkREADME.sh so the README picks up its usage message rather than the argparse error that -verbose=2 would produce. Its tests are also wired into the test target directly. testAll iterates ALL_APPS, which does not include USER_APP_SCRIPTS, so none of these programs' tests have ever been reachable from "make test" - that is why the suite sitting next to expMatrixToBarchartBed never reported it was broken. The makefile already keeps a short list of directories testAll cannot reach, and this adds two more to it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> diff --git src/utils/makefile src/utils/makefile index d9e29c8a34a..495d6e7cf96 100644 --- src/utils/makefile +++ src/utils/makefile @@ -1,308 +1,312 @@ # Build all directories in utils kentSrc = .. include ${kentSrc}/inc/localEnvironment.mk include ${kentSrc}/inc/common.mk # note: lists such as the following need to be defined *before* # they are used in the wildcard target rules. An oddity of gnu make # define the list of user applications to build # These will be distributed as part of the user apps build and we provide them # as binaries and collect usage messages # These are C programs, so make clean will be run UTILS_APPLIST = \ addCols \ ave \ aveCols \ bamToPsl \ bedClip \ bedGraphToBigWig \ bedJoinTabOffset \ bedToBigBed \ bigBedInfo \ bigBedNamedItems \ bigBedSummary \ bigBedToBed \ bedCommonRegions \ bedGeneParts \ bedGraphPack \ bedPileUps \ bedRemoveOverlap \ bedRestrictToPositions \ bigWigAverageOverBed \ bigWigCat \ bigWigCorrelate \ bigWigCluster \ bigWigInfo \ bigWigMerge \ bigWigSummary \ bigWigToBedGraph \ bigWigToWig \ calc \ catDir \ catUncomment \ chopFaLines \ colTransform \ countChars \ endsInLf \ clusterMatrixToBarChartBed \ cpgIslandExt \ faAlign \ fastqToFa \ fastqStatsAndSubsample \ faCmp \ faCount \ faFilterN \ faFilter \ faFrag \ faNoise \ faOneRecord \ faPolyASizes \ faRandomize \ faRc \ faSize \ faSomeRecords \ faSplit \ faToFastq \ faToTab \ faToTwoBit \ faTrans \ findMotif \ headRest \ htmlCheck \ matrixClusterColumns \ matrixMarketToTsv \ matrixNormalize \ matrixToBarChartBed \ newProg \ newPythonProg \ nibFrag \ nibSize \ pafToPsl \ paraFetch \ paraSync \ pslMap \ pslMapPostChain \ pslPosTarget \ pslProtToRnaCoords \ pslRc \ pslRemoveFrameShifts \ pslScore \ pslSpliceJunctions \ pslSwap \ pslToPslx \ randomLines \ raToTab \ raToLines \ rmFaDups \ rowsToCols \ sizeof \ spacedToTab \ splitFile \ splitFileByColumn \ strexCalc \ stringify \ subChar \ subColumn \ tabFmt \ tailLines \ textHistogram \ tickToDate \ timing \ toLower \ toUpper \ trackDbIndexBb \ twoBitDup \ twoBitInfo \ twoBitToFa \ wigCorrelate \ wigToBigWig \ wordLine \ # list of utilities to build of interest only at UCSC # These are C tools and will run a make clean on each # These are not part of the user apps build. UCSC_APPS = \ addCols \ aNotB \ aveCols \ ccCp \ convolve \ detab \ dnsInfo \ faFlyBaseToUcsc \ faGapLocs \ faGapSizes \ faNcbiToUcsc \ faRenameRecords \ faSimplify \ faToNib \ faTrimPolyA \ faTrimRead \ fixCr \ gapSplit \ gitTools \ gffPeek \ git-reports \ htmlPics \ jkUniq \ lineCount \ nt4Frag \ pslToXa \ scrambleFa \ subs \ tabToMmHash \ tableSum \ textHist2 \ udcCleanup \ undupFa \ upper \ vcfFilter \ venn \ verticalSplitSqlTable \ weedLines # These are parts of the user apps build, so they will land on hgdownload # These are not C programs, so no clean up USER_APP_SCRIPTS = \ bedJoinTabOffset.py \ expMatrixToBarchartBed \ + barChartReorder \ barChartMaxLimit \ ucscApiClient \ tdbRename \ tdbSort \ webSync \ chromToUcsc \ bigHeat \ bigGuessDb \ hubtools # Scripts that are not distributed outside of UCSC # They are not part of the user-apps build SCRIPT_FILES = \ agpToLift \ apacheLogParse \ bedCollapse.pl \ bedFixBlockOverlaps \ bedOverlapMerge \ bedSingleCover.pl \ bedBetween \ doLocusName \ extToolsChromeParse \ iSync \ lodToBedScore \ matrixMerge \ mkMafFrames.pl \ patSeqFilterBulkAndAnnotate \ patSeqSummarizeDocs \ pslProtCnv \ pslSameGene \ tabRepl \ uniprotToTab \ ggTables \ ggGeneClasses \ ggGpmlToTab \ ggKgmlToTab \ ggMsrToTab \ ggPidToTab \ ggPpiToTab \ genePredCompare \ ggSpfToTab \ bedNamePickFirst \ bedBestTranscript \ genePredToBed \ cgiSmokeTest \ phegenToBed \ bigMaxPercDiff \ cancerMafToBigBed \ pq \ bedAppendPaperInfo \ googleSheetToBigBed \ doClinvarLift \ codeReviewAi.py \ redmineCli \ browserRace \ ts \ ${USER_APP_SCRIPTS} # List of all directories to build ALL_APPS = $(UTILS_APPLIST) $(UCSC_APPS) # all: builds all utilities here all: $(ALL_APPS:%=%.all) $(USER_APP_SCRIPTS:%=%.userAppScript) %.all: cd $* && echo $* && $(MAKE) # userApps: builds the user application specific programs .PHONY: userApps userApps: $(UTILS_APPLIST:%=%.userApp) $(USER_APP_SCRIPTS:%=%.userAppScript) %.userApp: cd $* && echo $* && $(MAKE) %.userAppScript: @rm -f ${DESTDIR}${BINDIR}/$* @if test -d $* ; \ then \ chmod +x $*/$*; \ echo cp -p $*/$* ${DESTDIR}${BINDIR}; \ cp -p $*/$* ${DESTDIR}${BINDIR}; \ else \ chmod +x $*; \ echo cp -p $*/$* ${DESTDIR}${BINDIR}; \ cp -p $* ${DESTDIR}${BINDIR}/$*; \ fi scripts: $(SCRIPT_FILES:%=%.scripts) %.scripts: @rm -f ${SCRIPTS}/$* @if test -d $* ; \ then \ chmod +x $*/$*; \ echo cp -p $*/$* ${SCRIPTS}; \ cp -p $*/$* ${SCRIPTS}; \ else \ chmod +x $*; \ echo cp -p $* ${SCRIPTS}; \ cp -p $* ${SCRIPTS}; \ fi testAll: $(ALL_APPS:%=%.testAll) %.testAll: @test -s $*/tests/makefile && (echo $*; cd $* && $(MAKE) test) || true test: testAll cd faToTwoBit && ${MAKE} test cd twoBitToFa && ${MAKE} test cd twoBitInfo && ${MAKE} test cd bedGeneParts && ${MAKE} test # testRegistry is not an app, so the testAll rule above cannot reach it. Its test checks # that every row of the ticket-to-test registry still names a test that is in the tree, # refs #38391. cd testRegistry && ${MAKE} test +# USER_APP_SCRIPTS are not in ALL_APPS either, so testAll cannot reach their tests. + cd barChartReorder && ${MAKE} test + cd expMatrixToBarchartBed && ${MAKE} test clean: $(ALL_APPS:%=%.clean) touch non-empty-rm.o - find . -name \*.o -print | xargs rm %.clean: cd $* && echo $* && $(MAKE) clean BAD_DIRS= \ ccCpLock \ est2genomeToPsl \ geneStarts \ jimgrep \ jkShell \ wigAsciiToBinary \ cCp