diff options
Diffstat (limited to 'biology')
48 files changed, 730 insertions, 263 deletions
diff --git a/biology/augustus/Makefile b/biology/augustus/Makefile index 147d25ad6850..9ca5a108bdec 100644 --- a/biology/augustus/Makefile +++ b/biology/augustus/Makefile @@ -1,7 +1,7 @@ PORTNAME= augustus DISTVERSIONPREFIX= v DISTVERSION= 3.5.0 -PORTREVISION= 14 +PORTREVISION= 15 CATEGORIES= biology science PKGNAMESUFFIX= -gene-prediction diff --git a/biology/bbmap/Makefile b/biology/bbmap/Makefile index f9adfeb4db4f..533216187a45 100644 --- a/biology/bbmap/Makefile +++ b/biology/bbmap/Makefile @@ -1,5 +1,5 @@ PORTNAME= bbmap -DISTVERSION= 39.15 +DISTVERSION= 39.34 CATEGORIES= biology java MASTER_SITES= SF/bbmap/ DISTNAME= BBMap_${PORTVERSION} @@ -14,8 +14,8 @@ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/license.txt RUN_DEPENDS= bash:shells/bash \ - pigz:archivers/pigz \ - pbzip2:archivers/pbzip2 + pbzip2:archivers/pbzip2 \ + pigz:archivers/pigz USES= java shebangfix diff --git a/biology/bbmap/distinfo b/biology/bbmap/distinfo index 1bec09ddc1f9..c65e1b09d3ef 100644 --- a/biology/bbmap/distinfo +++ b/biology/bbmap/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1737030117 -SHA256 (BBMap_39.15.tar.gz) = b6698469a2a90f4930537c575ff1f70332f88a933dd5e286c83ea0ff30802344 -SIZE (BBMap_39.15.tar.gz) = 12498916 +TIMESTAMP = 1755776772 +SHA256 (BBMap_39.34.tar.gz) = c9c096c6ce3cc87da5607b731532bb9ac0aaebea2bd8fbf0a56e235968c4fbf4 +SIZE (BBMap_39.34.tar.gz) = 13743574 diff --git a/biology/bbmap/pkg-plist b/biology/bbmap/pkg-plist index 1515769118ae..6dc7649290c2 100644 --- a/biology/bbmap/pkg-plist +++ b/biology/bbmap/pkg-plist @@ -11,11 +11,14 @@ libexec/bbmap/a_sample_mt.sh libexec/bbmap/addadapters.sh libexec/bbmap/addssu.sh libexec/bbmap/adjusthomopolymers.sh +libexec/bbmap/alignrandom.sh libexec/bbmap/alltoall.sh libexec/bbmap/analyzeaccession.sh libexec/bbmap/analyzegenes.sh libexec/bbmap/analyzesketchresults.sh libexec/bbmap/applyvariants.sh +libexec/bbmap/bandedaligner.sh +libexec/bbmap/bandedplusaligner.sh libexec/bbmap/bbcms.sh libexec/bbmap/bbcountunique.sh libexec/bbmap/bbcrisprfinder.sh @@ -45,8 +48,10 @@ libexec/bbmap/callgenes.sh libexec/bbmap/callpeaks.sh libexec/bbmap/callvariants.sh libexec/bbmap/callvariants2.sh +libexec/bbmap/cat.sh libexec/bbmap/cg2illumina.sh libexec/bbmap/checkstrand.sh +libexec/bbmap/cladeloader.sh libexec/bbmap/clumpify.sh libexec/bbmap/commonkmers.sh libexec/bbmap/comparegff.sh @@ -64,6 +69,7 @@ libexec/bbmap/countgc.sh libexec/bbmap/countsharedlines.sh libexec/bbmap/crossblock.sh libexec/bbmap/crosscontaminate.sh +libexec/bbmap/crosscutaligner.sh libexec/bbmap/cutgff.sh libexec/bbmap/cutprimers.sh libexec/bbmap/decontaminate.sh @@ -73,6 +79,8 @@ libexec/bbmap/dedupebymapping.sh libexec/bbmap/demuxbyname.sh libexec/bbmap/demuxserver.sh libexec/bbmap/diskbench.sh +libexec/bbmap/driftingaligner.sh +libexec/bbmap/driftingplusaligner.sh libexec/bbmap/estherfilter.sh libexec/bbmap/explodetree.sh libexec/bbmap/fetchproks.sh @@ -98,6 +106,8 @@ libexec/bbmap/getreads.sh libexec/bbmap/gi2ancestors.sh libexec/bbmap/gi2taxid.sh libexec/bbmap/gitable.sh +libexec/bbmap/glocalaligner.sh +libexec/bbmap/gradebins.sh libexec/bbmap/grademerge.sh libexec/bbmap/gradesam.sh libexec/bbmap/icecreamfinder.sh @@ -105,7 +115,9 @@ libexec/bbmap/icecreamgrader.sh libexec/bbmap/icecreammaker.sh libexec/bbmap/idmatrix.sh libexec/bbmap/idtree.sh +libexec/bbmap/indelfree.sh libexec/bbmap/invertkey.sh +libexec/bbmap/javasetup.sh libexec/bbmap/kapastats.sh libexec/bbmap/kcompress.sh libexec/bbmap/keepbestcopy.sh @@ -124,8 +136,10 @@ libexec/bbmap/loglog.sh libexec/bbmap/makechimeras.sh libexec/bbmap/makecontaminatedgenomes.sh libexec/bbmap/makepolymers.sh +libexec/bbmap/makequickbinvector.sh libexec/bbmap/mapPacBio.sh libexec/bbmap/matrixtocolumns.sh +libexec/bbmap/memdetect.sh libexec/bbmap/mergeOTUs.sh libexec/bbmap/mergebarcodes.sh libexec/bbmap/mergepgm.sh @@ -133,6 +147,7 @@ libexec/bbmap/mergeribo.sh libexec/bbmap/mergesam.sh libexec/bbmap/mergesketch.sh libexec/bbmap/mergesorted.sh +libexec/bbmap/microalign.sh libexec/bbmap/msa.sh libexec/bbmap/mutate.sh libexec/bbmap/muxbyname.sh @@ -153,11 +168,16 @@ libexec/bbmap/printtime.sh libexec/bbmap/processfrag.sh libexec/bbmap/processhi-c.sh libexec/bbmap/processspeed.sh +libexec/bbmap/quabblealigner.sh +libexec/bbmap/quantumaligner.sh libexec/bbmap/quickbin.sh +libexec/bbmap/quickclade.sh libexec/bbmap/randomgenome.sh libexec/bbmap/randomreads.sh +libexec/bbmap/randomreadsmg.sh libexec/bbmap/readlength.sh libexec/bbmap/readqc.sh +libexec/bbmap/reducecolumns.sh libexec/bbmap/reducesilva.sh libexec/bbmap/reformat.sh libexec/bbmap/reformatpb.sh @@ -168,7 +188,10 @@ libexec/bbmap/removehuman2.sh libexec/bbmap/removemicrobes.sh libexec/bbmap/removesmartbell.sh libexec/bbmap/rename.sh +libexec/bbmap/renamebymapping.sh +libexec/bbmap/renamebysketch.sh libexec/bbmap/renameimg.sh +libexec/bbmap/renameref.sh libexec/bbmap/repair.sh libexec/bbmap/replaceheaders.sh libexec/bbmap/representative.sh @@ -195,6 +218,7 @@ libexec/bbmap/splitsam.sh libexec/bbmap/splitsam4way.sh libexec/bbmap/splitsam6way.sh libexec/bbmap/stats.sh +libexec/bbmap/stats3.sh libexec/bbmap/statswrapper.sh libexec/bbmap/streamsam.sh libexec/bbmap/subsketch.sh @@ -215,6 +239,8 @@ libexec/bbmap/taxonomy.sh libexec/bbmap/taxserver.sh libexec/bbmap/taxsize.sh libexec/bbmap/taxtree.sh +libexec/bbmap/testaligners.sh +libexec/bbmap/testaligners2.sh libexec/bbmap/testfilesystem.sh libexec/bbmap/testformat.sh libexec/bbmap/testformat2.sh @@ -227,7 +253,11 @@ libexec/bbmap/trimcontigs.sh libexec/bbmap/unicode2ascii.sh libexec/bbmap/unzip.sh libexec/bbmap/vcf2gff.sh +libexec/bbmap/visualizealignment.sh +libexec/bbmap/wavefrontaligner.sh libexec/bbmap/webcheck.sh +libexec/bbmap/wobblealigner.sh +libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/align2/AbstractIndex.class %%JAVAJARDIR%%/bbmap/align2/AbstractIndex.java %%JAVAJARDIR%%/bbmap/align2/AbstractMapThread.class @@ -348,9 +378,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/align2/QuadHeap.java %%JAVAJARDIR%%/bbmap/align2/QualityTools.class %%JAVAJARDIR%%/bbmap/align2/QualityTools.java -%%JAVAJARDIR%%/bbmap/align2/RandomReads3$1.class -%%JAVAJARDIR%%/bbmap/align2/RandomReads3.class -%%JAVAJARDIR%%/bbmap/align2/RandomReads3.java +%%JAVAJARDIR%%/bbmap/align2/README.md %%JAVAJARDIR%%/bbmap/align2/RefToIndex.class %%JAVAJARDIR%%/bbmap/align2/RefToIndex.java %%JAVAJARDIR%%/bbmap/align2/ReformatBatchOutput.class @@ -363,6 +391,9 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/align2/SplitMappedReads.java %%JAVAJARDIR%%/bbmap/align2/TranslateColorspaceRead.class %%JAVAJARDIR%%/bbmap/align2/TranslateColorspaceRead.java +%%JAVAJARDIR%%/bbmap/aligner/AlignRandom$1.class +%%JAVAJARDIR%%/bbmap/aligner/AlignRandom.class +%%JAVAJARDIR%%/bbmap/aligner/AlignRandom.java %%JAVAJARDIR%%/bbmap/aligner/Aligner.class %%JAVAJARDIR%%/bbmap/aligner/Aligner.java %%JAVAJARDIR%%/bbmap/aligner/Alignment.class @@ -372,10 +403,84 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/aligner/AllToAll$ProcessThread.class %%JAVAJARDIR%%/bbmap/aligner/AllToAll.class %%JAVAJARDIR%%/bbmap/aligner/AllToAll.java +%%JAVAJARDIR%%/bbmap/aligner/BandedAligner.class +%%JAVAJARDIR%%/bbmap/aligner/BandedAligner.java +%%JAVAJARDIR%%/bbmap/aligner/BandedAlignerConcise.class +%%JAVAJARDIR%%/bbmap/aligner/BandedAlignerConcise.java +%%JAVAJARDIR%%/bbmap/aligner/BandedAlignerInt.class +%%JAVAJARDIR%%/bbmap/aligner/BandedAlignerInt.java +%%JAVAJARDIR%%/bbmap/aligner/BandedAlignerM.class +%%JAVAJARDIR%%/bbmap/aligner/BandedAlignerM.java +%%JAVAJARDIR%%/bbmap/aligner/BandedByteAligner.class +%%JAVAJARDIR%%/bbmap/aligner/BandedByteAligner.java +%%JAVAJARDIR%%/bbmap/aligner/BandedPlusAligner.class +%%JAVAJARDIR%%/bbmap/aligner/BandedPlusAligner.java +%%JAVAJARDIR%%/bbmap/aligner/BandedPlusAligner2.class +%%JAVAJARDIR%%/bbmap/aligner/BandedPlusAligner2.java +%%JAVAJARDIR%%/bbmap/aligner/BandedPlusAligner3.class +%%JAVAJARDIR%%/bbmap/aligner/BandedPlusAligner3.java +%%JAVAJARDIR%%/bbmap/aligner/BandedPlusAlignerInt.class +%%JAVAJARDIR%%/bbmap/aligner/BandedPlusAlignerInt.java +%%JAVAJARDIR%%/bbmap/aligner/ClippingTest.class +%%JAVAJARDIR%%/bbmap/aligner/ClippingTest.java +%%JAVAJARDIR%%/bbmap/aligner/CrossCutAligner.class +%%JAVAJARDIR%%/bbmap/aligner/CrossCutAligner.java +%%JAVAJARDIR%%/bbmap/aligner/DiagonalAligner$ExtzResult.class +%%JAVAJARDIR%%/bbmap/aligner/DiagonalAligner.class +%%JAVAJARDIR%%/bbmap/aligner/DiagonalAligner.java +%%JAVAJARDIR%%/bbmap/aligner/DriftingAligner.class +%%JAVAJARDIR%%/bbmap/aligner/DriftingAligner.java +%%JAVAJARDIR%%/bbmap/aligner/DriftingAlignerConcise.class +%%JAVAJARDIR%%/bbmap/aligner/DriftingAlignerConcise.java +%%JAVAJARDIR%%/bbmap/aligner/DriftingAlignerM.class +%%JAVAJARDIR%%/bbmap/aligner/DriftingAlignerM.java +%%JAVAJARDIR%%/bbmap/aligner/DriftingPlusAligner.class +%%JAVAJARDIR%%/bbmap/aligner/DriftingPlusAligner.java +%%JAVAJARDIR%%/bbmap/aligner/DriftingPlusAligner2.class +%%JAVAJARDIR%%/bbmap/aligner/DriftingPlusAligner2.java +%%JAVAJARDIR%%/bbmap/aligner/DriftingPlusAligner3.class +%%JAVAJARDIR%%/bbmap/aligner/DriftingPlusAligner3.java +%%JAVAJARDIR%%/bbmap/aligner/Eh.class +%%JAVAJARDIR%%/bbmap/aligner/Factory.class +%%JAVAJARDIR%%/bbmap/aligner/Factory.java %%JAVAJARDIR%%/bbmap/aligner/FlatAligner.class %%JAVAJARDIR%%/bbmap/aligner/FlatAligner.java %%JAVAJARDIR%%/bbmap/aligner/FlatAligner2.class %%JAVAJARDIR%%/bbmap/aligner/FlatAligner2.java +%%JAVAJARDIR%%/bbmap/aligner/GlocalAligner.class +%%JAVAJARDIR%%/bbmap/aligner/GlocalAligner.java +%%JAVAJARDIR%%/bbmap/aligner/GlocalAlignerConcise.class +%%JAVAJARDIR%%/bbmap/aligner/GlocalAlignerConcise.java +%%JAVAJARDIR%%/bbmap/aligner/GlocalAlignerInt.class +%%JAVAJARDIR%%/bbmap/aligner/GlocalAlignerInt.java +%%JAVAJARDIR%%/bbmap/aligner/GlocalAlignerOld.class +%%JAVAJARDIR%%/bbmap/aligner/GlocalAlignerOld.java +%%JAVAJARDIR%%/bbmap/aligner/GlocalPlusAligner.class +%%JAVAJARDIR%%/bbmap/aligner/GlocalPlusAligner.java +%%JAVAJARDIR%%/bbmap/aligner/GlocalPlusAligner2.class +%%JAVAJARDIR%%/bbmap/aligner/GlocalPlusAligner2.java +%%JAVAJARDIR%%/bbmap/aligner/GlocalPlusAligner3.class +%%JAVAJARDIR%%/bbmap/aligner/GlocalPlusAligner3.java +%%JAVAJARDIR%%/bbmap/aligner/GlocalPlusAligner4.class +%%JAVAJARDIR%%/bbmap/aligner/GlocalPlusAligner4.java +%%JAVAJARDIR%%/bbmap/aligner/GlocalPlusAligner5.class +%%JAVAJARDIR%%/bbmap/aligner/GlocalPlusAligner5.java +%%JAVAJARDIR%%/bbmap/aligner/IDAligner.class +%%JAVAJARDIR%%/bbmap/aligner/IDAligner.java +%%JAVAJARDIR%%/bbmap/aligner/IndelFreeAligner$ProcessThread.class +%%JAVAJARDIR%%/bbmap/aligner/IndelFreeAligner.class +%%JAVAJARDIR%%/bbmap/aligner/IndelFreeAligner.java +%%JAVAJARDIR%%/bbmap/aligner/IntIndex.class +%%JAVAJARDIR%%/bbmap/aligner/IntIndex.java +%%JAVAJARDIR%%/bbmap/aligner/IntListAligner.class +%%JAVAJARDIR%%/bbmap/aligner/IntListAligner.java +%%JAVAJARDIR%%/bbmap/aligner/Ksw2gg$Cell.class +%%JAVAJARDIR%%/bbmap/aligner/Ksw2gg.class +%%JAVAJARDIR%%/bbmap/aligner/Ksw2gg.java +%%JAVAJARDIR%%/bbmap/aligner/KswGgJava.class +%%JAVAJARDIR%%/bbmap/aligner/KswGgJava.java +%%JAVAJARDIR%%/bbmap/aligner/MSAViz.class +%%JAVAJARDIR%%/bbmap/aligner/MSAViz.java %%JAVAJARDIR%%/bbmap/aligner/MicroAligner.class %%JAVAJARDIR%%/bbmap/aligner/MicroAligner.java %%JAVAJARDIR%%/bbmap/aligner/MicroAligner2.class @@ -384,6 +489,13 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/aligner/MicroAligner3.java %%JAVAJARDIR%%/bbmap/aligner/MicroIndex3.class %%JAVAJARDIR%%/bbmap/aligner/MicroIndex3.java +%%JAVAJARDIR%%/bbmap/aligner/MicroWrapper$ProcessThread.class +%%JAVAJARDIR%%/bbmap/aligner/MicroWrapper.class +%%JAVAJARDIR%%/bbmap/aligner/MicroWrapper.java +%%JAVAJARDIR%%/bbmap/aligner/MinHitsCalculator.class +%%JAVAJARDIR%%/bbmap/aligner/MinHitsCalculator.java +%%JAVAJARDIR%%/bbmap/aligner/MinHitsCalculatorOld.class +%%JAVAJARDIR%%/bbmap/aligner/MinHitsCalculatorOld.java %%JAVAJARDIR%%/bbmap/aligner/MultiStateAligner9PacBioAdapter.class %%JAVAJARDIR%%/bbmap/aligner/MultiStateAligner9PacBioAdapter.java %%JAVAJARDIR%%/bbmap/aligner/MultiStateAligner9PacBioAdapter2.class @@ -392,6 +504,35 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/aligner/MultiStateAligner9PacBioAdapter3.java %%JAVAJARDIR%%/bbmap/aligner/MultiStateAligner9PacBioAdapter_WithBarriers.class %%JAVAJARDIR%%/bbmap/aligner/MultiStateAligner9PacBioAdapter_WithBarriers.java +%%JAVAJARDIR%%/bbmap/aligner/Parallelogram.class +%%JAVAJARDIR%%/bbmap/aligner/Parallelogram.java +%%JAVAJARDIR%%/bbmap/aligner/QuabbleAligner.class +%%JAVAJARDIR%%/bbmap/aligner/QuabbleAligner.java +%%JAVAJARDIR%%/bbmap/aligner/QuantumAligner.class +%%JAVAJARDIR%%/bbmap/aligner/QuantumAligner.java +%%JAVAJARDIR%%/bbmap/aligner/QuantumAlignerConcise.class +%%JAVAJARDIR%%/bbmap/aligner/QuantumAlignerConcise.java +%%JAVAJARDIR%%/bbmap/aligner/QuantumAlignerConcise2.class +%%JAVAJARDIR%%/bbmap/aligner/QuantumAlignerConcise2.java +%%JAVAJARDIR%%/bbmap/aligner/QuantumAlignerM.class +%%JAVAJARDIR%%/bbmap/aligner/QuantumAlignerM.java +%%JAVAJARDIR%%/bbmap/aligner/QuantumAlignerQC.class +%%JAVAJARDIR%%/bbmap/aligner/QuantumAlignerQC.java +%%JAVAJARDIR%%/bbmap/aligner/QuantumPlusAligner.class +%%JAVAJARDIR%%/bbmap/aligner/QuantumPlusAligner.java +%%JAVAJARDIR%%/bbmap/aligner/QuantumPlusAligner2.class +%%JAVAJARDIR%%/bbmap/aligner/QuantumPlusAligner2.java +%%JAVAJARDIR%%/bbmap/aligner/QuantumPlusAligner3.class +%%JAVAJARDIR%%/bbmap/aligner/QuantumPlusAligner3.java +%%JAVAJARDIR%%/bbmap/aligner/QuantumPlusAligner4.class +%%JAVAJARDIR%%/bbmap/aligner/QuantumPlusAligner4.java +%%JAVAJARDIR%%/bbmap/aligner/Query.class +%%JAVAJARDIR%%/bbmap/aligner/Query.java +%%JAVAJARDIR%%/bbmap/aligner/README.md +%%JAVAJARDIR%%/bbmap/aligner/RelativeAligner.class +%%JAVAJARDIR%%/bbmap/aligner/RelativeAligner.java +%%JAVAJARDIR%%/bbmap/aligner/ScrabbleAligner.class +%%JAVAJARDIR%%/bbmap/aligner/ScrabbleAligner.java %%JAVAJARDIR%%/bbmap/aligner/SideChannel3.class %%JAVAJARDIR%%/bbmap/aligner/SideChannel3.java %%JAVAJARDIR%%/bbmap/aligner/SingleStateAlignerFlat.class @@ -408,6 +549,39 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/aligner/SingleStateAlignerFlatFloat.java %%JAVAJARDIR%%/bbmap/aligner/SingleStateAlignerPacBioAdapter.class %%JAVAJARDIR%%/bbmap/aligner/SingleStateAlignerPacBioAdapter.java +%%JAVAJARDIR%%/bbmap/aligner/Test$Runner.class +%%JAVAJARDIR%%/bbmap/aligner/Test.class +%%JAVAJARDIR%%/bbmap/aligner/Test.java +%%JAVAJARDIR%%/bbmap/aligner/TestAlignerSuite$Job.class +%%JAVAJARDIR%%/bbmap/aligner/TestAlignerSuite$Worker.class +%%JAVAJARDIR%%/bbmap/aligner/TestAlignerSuite.class +%%JAVAJARDIR%%/bbmap/aligner/TestAlignerSuite.java +%%JAVAJARDIR%%/bbmap/aligner/VisualizationConverter.class +%%JAVAJARDIR%%/bbmap/aligner/VisualizationConverter.java +%%JAVAJARDIR%%/bbmap/aligner/Visualizer.class +%%JAVAJARDIR%%/bbmap/aligner/Visualizer.java +%%JAVAJARDIR%%/bbmap/aligner/WaveFrontAligner.class +%%JAVAJARDIR%%/bbmap/aligner/WaveFrontAligner.java +%%JAVAJARDIR%%/bbmap/aligner/WaveFrontAligner2.class +%%JAVAJARDIR%%/bbmap/aligner/WaveFrontAligner2.java +%%JAVAJARDIR%%/bbmap/aligner/WaveFrontAlignerViz.class +%%JAVAJARDIR%%/bbmap/aligner/WaveFrontAlignerViz.java +%%JAVAJARDIR%%/bbmap/aligner/WobbleAligner.class +%%JAVAJARDIR%%/bbmap/aligner/WobbleAligner.java +%%JAVAJARDIR%%/bbmap/aligner/WobbleAlignerConcise.class +%%JAVAJARDIR%%/bbmap/aligner/WobbleAlignerConcise.java +%%JAVAJARDIR%%/bbmap/aligner/WobblePlusAligner.class +%%JAVAJARDIR%%/bbmap/aligner/WobblePlusAligner.java +%%JAVAJARDIR%%/bbmap/aligner/WobblePlusAligner2.class +%%JAVAJARDIR%%/bbmap/aligner/WobblePlusAligner2.java +%%JAVAJARDIR%%/bbmap/aligner/WobblePlusAligner3.class +%%JAVAJARDIR%%/bbmap/aligner/WobblePlusAligner3.java +%%JAVAJARDIR%%/bbmap/aligner/WobblePlusAligner4.class +%%JAVAJARDIR%%/bbmap/aligner/WobblePlusAligner4.java +%%JAVAJARDIR%%/bbmap/aligner/WobblePlusAligner5.class +%%JAVAJARDIR%%/bbmap/aligner/WobblePlusAligner5.java +%%JAVAJARDIR%%/bbmap/aligner/XDropHAligner.class +%%JAVAJARDIR%%/bbmap/aligner/XDropHAligner.java %%JAVAJARDIR%%/bbmap/assemble/AbstractBuildThread.class %%JAVAJARDIR%%/bbmap/assemble/AbstractBuildThread.java %%JAVAJARDIR%%/bbmap/assemble/AbstractExploreThread.class @@ -433,6 +607,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/assemble/KmerCompressor.java %%JAVAJARDIR%%/bbmap/assemble/Postfilter.class %%JAVAJARDIR%%/bbmap/assemble/Postfilter.java +%%JAVAJARDIR%%/bbmap/assemble/README.md %%JAVAJARDIR%%/bbmap/assemble/Rollback.class %%JAVAJARDIR%%/bbmap/assemble/Rollback.java %%JAVAJARDIR%%/bbmap/assemble/ShaveObject.class @@ -508,6 +683,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/barcode/PCRMatrixHDist$PopThread.class %%JAVAJARDIR%%/bbmap/barcode/PCRMatrixHDist.class %%JAVAJARDIR%%/bbmap/barcode/PCRMatrixHDist.java +%%JAVAJARDIR%%/bbmap/barcode/README.md %%JAVAJARDIR%%/bbmap/barcode/TagAndMerge.class %%JAVAJARDIR%%/bbmap/barcode/TagAndMerge.java %%JAVAJARDIR%%/bbmap/barcode/Transition.class @@ -520,40 +696,124 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/barcode/stub/PCRMatrixTile.java %%JAVAJARDIR%%/bbmap/bbmin/Minimizer.class %%JAVAJARDIR%%/bbmap/bbmin/Minimizer.java +%%JAVAJARDIR%%/bbmap/bbmin/README.md +%%JAVAJARDIR%%/bbmap/bin/AbstractRefiner$EnsembleRefinerParams.class +%%JAVAJARDIR%%/bbmap/bin/AbstractRefiner$EvidenceRefinerParams.class +%%JAVAJARDIR%%/bbmap/bin/AbstractRefiner$GraphRefinerParams.class +%%JAVAJARDIR%%/bbmap/bin/AbstractRefiner$RefinerParams.class +%%JAVAJARDIR%%/bbmap/bin/AbstractRefiner.class +%%JAVAJARDIR%%/bbmap/bin/AbstractRefiner.java +%%JAVAJARDIR%%/bbmap/bin/AdjustEntropy.class +%%JAVAJARDIR%%/bbmap/bin/AdjustEntropy.java +%%JAVAJARDIR%%/bbmap/bin/AllToAllVectorMaker.class +%%JAVAJARDIR%%/bbmap/bin/AllToAllVectorMaker.java %%JAVAJARDIR%%/bbmap/bin/Bin.class %%JAVAJARDIR%%/bbmap/bin/Bin.java +%%JAVAJARDIR%%/bbmap/bin/BinComparator.class +%%JAVAJARDIR%%/bbmap/bin/BinComparator.java +%%JAVAJARDIR%%/bbmap/bin/BinMap.class +%%JAVAJARDIR%%/bbmap/bin/BinMap.java %%JAVAJARDIR%%/bbmap/bin/BinObject.class %%JAVAJARDIR%%/bbmap/bin/BinObject.java %%JAVAJARDIR%%/bbmap/bin/BinSketcher$ProcessThread.class %%JAVAJARDIR%%/bbmap/bin/BinSketcher.class %%JAVAJARDIR%%/bbmap/bin/BinSketcher.java +%%JAVAJARDIR%%/bbmap/bin/BinStats.class +%%JAVAJARDIR%%/bbmap/bin/BinStats.java +%%JAVAJARDIR%%/bbmap/bin/BinStatsComparator.class +%%JAVAJARDIR%%/bbmap/bin/BinStatsComparator.java +%%JAVAJARDIR%%/bbmap/bin/Binner$CompareThread.class %%JAVAJARDIR%%/bbmap/bin/Binner.class %%JAVAJARDIR%%/bbmap/bin/Binner.java +%%JAVAJARDIR%%/bbmap/bin/ChartMaker.class +%%JAVAJARDIR%%/bbmap/bin/ChartMaker.java +%%JAVAJARDIR%%/bbmap/bin/Clade.class +%%JAVAJARDIR%%/bbmap/bin/Clade.java +%%JAVAJARDIR%%/bbmap/bin/CladeIndex.class +%%JAVAJARDIR%%/bbmap/bin/CladeIndex.java +%%JAVAJARDIR%%/bbmap/bin/CladeLoader$ProcessThread.class +%%JAVAJARDIR%%/bbmap/bin/CladeLoader.class +%%JAVAJARDIR%%/bbmap/bin/CladeLoader.java +%%JAVAJARDIR%%/bbmap/bin/CladeLoaderMF$ProcessThread.class +%%JAVAJARDIR%%/bbmap/bin/CladeLoaderMF.class +%%JAVAJARDIR%%/bbmap/bin/CladeLoaderMF.java +%%JAVAJARDIR%%/bbmap/bin/CladeSearcher$ProcessThread.class +%%JAVAJARDIR%%/bbmap/bin/CladeSearcher.class +%%JAVAJARDIR%%/bbmap/bin/CladeSearcher.java %%JAVAJARDIR%%/bbmap/bin/Cluster.class %%JAVAJARDIR%%/bbmap/bin/Cluster.java +%%JAVAJARDIR%%/bbmap/bin/Comparison.class +%%JAVAJARDIR%%/bbmap/bin/Comparison.java +%%JAVAJARDIR%%/bbmap/bin/ComparisonHeap$WorstFirstComparator.class +%%JAVAJARDIR%%/bbmap/bin/ComparisonHeap.class +%%JAVAJARDIR%%/bbmap/bin/ComparisonHeap.java +%%JAVAJARDIR%%/bbmap/bin/ConservationModel.class +%%JAVAJARDIR%%/bbmap/bin/ConservationModel.java +%%JAVAJARDIR%%/bbmap/bin/Contig$ContigIterator.class %%JAVAJARDIR%%/bbmap/bin/Contig.class %%JAVAJARDIR%%/bbmap/bin/Contig.java %%JAVAJARDIR%%/bbmap/bin/ContigRenamer$ProcessThread.class %%JAVAJARDIR%%/bbmap/bin/ContigRenamer$Scaf.class %%JAVAJARDIR%%/bbmap/bin/ContigRenamer.class %%JAVAJARDIR%%/bbmap/bin/ContigRenamer.java +%%JAVAJARDIR%%/bbmap/bin/CrystalChamber$Centroid.class +%%JAVAJARDIR%%/bbmap/bin/CrystalChamber.class +%%JAVAJARDIR%%/bbmap/bin/CrystalChamber.java +%%JAVAJARDIR%%/bbmap/bin/CrystalChamber2$Centroid.class +%%JAVAJARDIR%%/bbmap/bin/CrystalChamber2.class +%%JAVAJARDIR%%/bbmap/bin/CrystalChamber2.java %%JAVAJARDIR%%/bbmap/bin/DataLoader.class %%JAVAJARDIR%%/bbmap/bin/DataLoader.java +%%JAVAJARDIR%%/bbmap/bin/EnsembleRefiner$ConsensusResult.class +%%JAVAJARDIR%%/bbmap/bin/EnsembleRefiner$RefinerResult.class +%%JAVAJARDIR%%/bbmap/bin/EnsembleRefiner.class +%%JAVAJARDIR%%/bbmap/bin/EnsembleRefiner.java +%%JAVAJARDIR%%/bbmap/bin/EvidenceRefiner$ContigStatus.class +%%JAVAJARDIR%%/bbmap/bin/EvidenceRefiner$DBSCANResult.class +%%JAVAJARDIR%%/bbmap/bin/EvidenceRefiner.class +%%JAVAJARDIR%%/bbmap/bin/EvidenceRefiner.java %%JAVAJARDIR%%/bbmap/bin/FileRenamer.class %%JAVAJARDIR%%/bbmap/bin/FileRenamer.java +%%JAVAJARDIR%%/bbmap/bin/GTDBLine.class +%%JAVAJARDIR%%/bbmap/bin/GTDBLine.java +%%JAVAJARDIR%%/bbmap/bin/GeneTools.class +%%JAVAJARDIR%%/bbmap/bin/GeneTools.java +%%JAVAJARDIR%%/bbmap/bin/GradeBins$CCLine.class +%%JAVAJARDIR%%/bbmap/bin/GradeBins$ProcessThread.class +%%JAVAJARDIR%%/bbmap/bin/GradeBins.class +%%JAVAJARDIR%%/bbmap/bin/GradeBins.java +%%JAVAJARDIR%%/bbmap/bin/GraphRefiner$SimilarityGraph$Edge.class +%%JAVAJARDIR%%/bbmap/bin/GraphRefiner$SimilarityGraph.class +%%JAVAJARDIR%%/bbmap/bin/GraphRefiner.class +%%JAVAJARDIR%%/bbmap/bin/GraphRefiner.java +%%JAVAJARDIR%%/bbmap/bin/IDComparator.class +%%JAVAJARDIR%%/bbmap/bin/IDComparator.java +%%JAVAJARDIR%%/bbmap/bin/Key.class +%%JAVAJARDIR%%/bbmap/bin/Key.java +%%JAVAJARDIR%%/bbmap/bin/KeyValue.class +%%JAVAJARDIR%%/bbmap/bin/KeyValue.java +%%JAVAJARDIR%%/bbmap/bin/KmerProb.class +%%JAVAJARDIR%%/bbmap/bin/KmerProb.java +%%JAVAJARDIR%%/bbmap/bin/Oracle.class +%%JAVAJARDIR%%/bbmap/bin/Oracle.java %%JAVAJARDIR%%/bbmap/bin/QuickBin$ProcessThread.class %%JAVAJARDIR%%/bbmap/bin/QuickBin.class %%JAVAJARDIR%%/bbmap/bin/QuickBin.java -%%JAVAJARDIR%%/bbmap/bin/RandomReadsMG$Genome.class -%%JAVAJARDIR%%/bbmap/bin/RandomReadsMG$ProcessThread.class -%%JAVAJARDIR%%/bbmap/bin/RandomReadsMG.class -%%JAVAJARDIR%%/bbmap/bin/RandomReadsMG.java +%%JAVAJARDIR%%/bbmap/bin/README.md +%%JAVAJARDIR%%/bbmap/bin/SamLoader$LoadThread.class +%%JAVAJARDIR%%/bbmap/bin/SamLoader.class +%%JAVAJARDIR%%/bbmap/bin/SamLoader.java +%%JAVAJARDIR%%/bbmap/bin/ScoreComparator.class +%%JAVAJARDIR%%/bbmap/bin/ScoreComparator.java %%JAVAJARDIR%%/bbmap/bin/SimilarityMeasures.class %%JAVAJARDIR%%/bbmap/bin/SimilarityMeasures.java %%JAVAJARDIR%%/bbmap/bin/SketchRecord.class %%JAVAJARDIR%%/bbmap/bin/SketchRecord.java %%JAVAJARDIR%%/bbmap/bin/Sketchable.class %%JAVAJARDIR%%/bbmap/bin/Sketchable.java +%%JAVAJARDIR%%/bbmap/bin/SpectraCounter$LoadThread.class +%%JAVAJARDIR%%/bbmap/bin/SpectraCounter.class +%%JAVAJARDIR%%/bbmap/bin/SpectraCounter.java %%JAVAJARDIR%%/bbmap/bloom/BloomFilter.class %%JAVAJARDIR%%/bbmap/bloom/BloomFilter.java %%JAVAJARDIR%%/bbmap/bloom/BloomFilterCorrector.class @@ -616,6 +876,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/bloom/PolyFilter$ProcessThread.class %%JAVAJARDIR%%/bbmap/bloom/PolyFilter.class %%JAVAJARDIR%%/bbmap/bloom/PolyFilter.java +%%JAVAJARDIR%%/bbmap/bloom/README.md %%JAVAJARDIR%%/bbmap/bloom/ReadCounter$1.class %%JAVAJARDIR%%/bbmap/bloom/ReadCounter$CountThread.class %%JAVAJARDIR%%/bbmap/bloom/ReadCounter.class @@ -651,6 +912,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/cardinality/LogLog_old.java %%JAVAJARDIR%%/bbmap/cardinality/MultiLogLog.class %%JAVAJARDIR%%/bbmap/cardinality/MultiLogLog.java +%%JAVAJARDIR%%/bbmap/cardinality/README.md %%JAVAJARDIR%%/bbmap/clump/Clump.class %%JAVAJARDIR%%/bbmap/clump/Clump.java %%JAVAJARDIR%%/bbmap/clump/ClumpList$ClumpThread.class @@ -693,6 +955,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/clump/PivotSet$HashThread.class %%JAVAJARDIR%%/bbmap/clump/PivotSet.class %%JAVAJARDIR%%/bbmap/clump/PivotSet.java +%%JAVAJARDIR%%/bbmap/clump/README.md %%JAVAJARDIR%%/bbmap/clump/ReadKey.class %%JAVAJARDIR%%/bbmap/clump/ReadKey.java %%JAVAJARDIR%%/bbmap/clump/Splitter.class @@ -705,6 +968,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/cluster/ClusterTools.java %%JAVAJARDIR%%/bbmap/cluster/MergeReadHeaders.class %%JAVAJARDIR%%/bbmap/cluster/MergeReadHeaders.java +%%JAVAJARDIR%%/bbmap/cluster/README.md %%JAVAJARDIR%%/bbmap/cluster/ReadTag.class %%JAVAJARDIR%%/bbmap/cluster/ReadTag.java %%JAVAJARDIR%%/bbmap/cluster/ReclusterByKmer$ClusterThread.class @@ -730,6 +994,8 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/consensus/Lilypad$ProcessThread.class %%JAVAJARDIR%%/bbmap/consensus/Lilypad.class %%JAVAJARDIR%%/bbmap/consensus/Lilypad.java +%%JAVAJARDIR%%/bbmap/consensus/README.md +%%JAVAJARDIR%%/bbmap/covid/README.md %%JAVAJARDIR%%/bbmap/covid/SummarizeCoverage.class %%JAVAJARDIR%%/bbmap/covid/SummarizeCoverage.java %%JAVAJARDIR%%/bbmap/dna/AminoAcid.class @@ -762,6 +1028,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/dna/MotifProbsN.java %%JAVAJARDIR%%/bbmap/dna/MotifSimple.class %%JAVAJARDIR%%/bbmap/dna/MotifSimple.java +%%JAVAJARDIR%%/bbmap/dna/README.md %%JAVAJARDIR%%/bbmap/dna/ScafLoc.class %%JAVAJARDIR%%/bbmap/dna/ScafLoc.java %%JAVAJARDIR%%/bbmap/dna/Scaffold.class @@ -853,6 +1120,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/driver/ProcessSpeed2.java %%JAVAJARDIR%%/bbmap/driver/ProcessWebcheck.class %%JAVAJARDIR%%/bbmap/driver/ProcessWebcheck.java +%%JAVAJARDIR%%/bbmap/driver/README.md %%JAVAJARDIR%%/bbmap/driver/ReduceSilva.class %%JAVAJARDIR%%/bbmap/driver/ReduceSilva.java %%JAVAJARDIR%%/bbmap/driver/RenameAndMux$MuxThread.class @@ -928,6 +1196,8 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/fileIO/ChainLine.java %%JAVAJARDIR%%/bbmap/fileIO/CompressFiles.class %%JAVAJARDIR%%/bbmap/fileIO/CompressFiles.java +%%JAVAJARDIR%%/bbmap/fileIO/Concatenate.class +%%JAVAJARDIR%%/bbmap/fileIO/Concatenate.java %%JAVAJARDIR%%/bbmap/fileIO/CopyFile$1.class %%JAVAJARDIR%%/bbmap/fileIO/CopyFile.class %%JAVAJARDIR%%/bbmap/fileIO/CopyFile.java @@ -951,6 +1221,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/fileIO/PipeThread.java %%JAVAJARDIR%%/bbmap/fileIO/QuickFile.class %%JAVAJARDIR%%/bbmap/fileIO/QuickFile.java +%%JAVAJARDIR%%/bbmap/fileIO/README.md %%JAVAJARDIR%%/bbmap/fileIO/ReadWrite$1.class %%JAVAJARDIR%%/bbmap/fileIO/ReadWrite$WriteObjectThread.class %%JAVAJARDIR%%/bbmap/fileIO/ReadWrite$WriteStringThread.class @@ -973,6 +1244,11 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/fun/DiskBench$WriteThread.class %%JAVAJARDIR%%/bbmap/fun/DiskBench.class %%JAVAJARDIR%%/bbmap/fun/DiskBench.java +%%JAVAJARDIR%%/bbmap/fun/DiskSpaceAnalyzer$1.class +%%JAVAJARDIR%%/bbmap/fun/DiskSpaceAnalyzer$2.class +%%JAVAJARDIR%%/bbmap/fun/DiskSpaceAnalyzer$DirSize.class +%%JAVAJARDIR%%/bbmap/fun/DiskSpaceAnalyzer.class +%%JAVAJARDIR%%/bbmap/fun/DiskSpaceAnalyzer.java %%JAVAJARDIR%%/bbmap/fun/Dongle.class %%JAVAJARDIR%%/bbmap/fun/Dongle.java %%JAVAJARDIR%%/bbmap/fun/FindPath$Edge.class @@ -1016,12 +1292,15 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/fun/Palindrome2$Drome.class %%JAVAJARDIR%%/bbmap/fun/Palindrome2.class %%JAVAJARDIR%%/bbmap/fun/Palindrome2.java +%%JAVAJARDIR%%/bbmap/fun/ParseDouble.class +%%JAVAJARDIR%%/bbmap/fun/ParseDouble.java %%JAVAJARDIR%%/bbmap/fun/ProbShared.class %%JAVAJARDIR%%/bbmap/fun/ProbShared.java %%JAVAJARDIR%%/bbmap/fun/ProbShared2.class %%JAVAJARDIR%%/bbmap/fun/ProbShared2.java %%JAVAJARDIR%%/bbmap/fun/ProbShared3.class %%JAVAJARDIR%%/bbmap/fun/ProbShared3.java +%%JAVAJARDIR%%/bbmap/fun/README.md %%JAVAJARDIR%%/bbmap/gff/CompareGff.class %%JAVAJARDIR%%/bbmap/gff/CompareGff.java %%JAVAJARDIR%%/bbmap/gff/CompareGff_old.class @@ -1039,8 +1318,11 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/gff/GbffLocus.java %%JAVAJARDIR%%/bbmap/gff/GffLine.class %%JAVAJARDIR%%/bbmap/gff/GffLine.java +%%JAVAJARDIR%%/bbmap/gff/GtfLine.class +%%JAVAJARDIR%%/bbmap/gff/GtfLine.java %%JAVAJARDIR%%/bbmap/gff/ParseCrispr.class %%JAVAJARDIR%%/bbmap/gff/ParseCrispr.java +%%JAVAJARDIR%%/bbmap/gff/README.md %%JAVAJARDIR%%/bbmap/gff/VcfToGff$1.class %%JAVAJARDIR%%/bbmap/gff/VcfToGff.class %%JAVAJARDIR%%/bbmap/gff/VcfToGff.java @@ -1075,6 +1357,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/hiseq/PlotHist.java %%JAVAJARDIR%%/bbmap/hiseq/PlotReadPosition.class %%JAVAJARDIR%%/bbmap/hiseq/PlotReadPosition.java +%%JAVAJARDIR%%/bbmap/hiseq/README.md %%JAVAJARDIR%%/bbmap/hiseq/ReadHeaderParser.class %%JAVAJARDIR%%/bbmap/hiseq/ReadHeaderParser.java %%JAVAJARDIR%%/bbmap/hiseq/Tile.class @@ -1087,6 +1370,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/hmm/HMMSearchReport.java %%JAVAJARDIR%%/bbmap/hmm/ProteinSummary.class %%JAVAJARDIR%%/bbmap/hmm/ProteinSummary.java +%%JAVAJARDIR%%/bbmap/hmm/README.md %%JAVAJARDIR%%/bbmap/icecream/IceCreamAligner.class %%JAVAJARDIR%%/bbmap/icecream/IceCreamAligner.java %%JAVAJARDIR%%/bbmap/icecream/IceCreamAlignerJNI.class @@ -1105,6 +1389,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/icecream/PBHeader.java %%JAVAJARDIR%%/bbmap/icecream/PolymerTrimmer.class %%JAVAJARDIR%%/bbmap/icecream/PolymerTrimmer.java +%%JAVAJARDIR%%/bbmap/icecream/README.md %%JAVAJARDIR%%/bbmap/icecream/ReadBuilder.class %%JAVAJARDIR%%/bbmap/icecream/ReadBuilder.java %%JAVAJARDIR%%/bbmap/icecream/ReformatPacBio$ProcessThread.class @@ -1114,49 +1399,22 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/icecream/ZMW.java %%JAVAJARDIR%%/bbmap/icecream/ZMWStreamer.class %%JAVAJARDIR%%/bbmap/icecream/ZMWStreamer.java -%%JAVAJARDIR%%/bbmap/jasper/Comparison.class -%%JAVAJARDIR%%/bbmap/jasper/Comparison.java -%%JAVAJARDIR%%/bbmap/jasper/DenseSimilarityMatrix.class -%%JAVAJARDIR%%/bbmap/jasper/DenseSimilarityMatrix.java -%%JAVAJARDIR%%/bbmap/jasper/DenseTree.class -%%JAVAJARDIR%%/bbmap/jasper/DenseTree.java -%%JAVAJARDIR%%/bbmap/jasper/DenseTreeValidate.class -%%JAVAJARDIR%%/bbmap/jasper/DenseTreeValidate.java %%JAVAJARDIR%%/bbmap/jasper/KmerPosition.class %%JAVAJARDIR%%/bbmap/jasper/KmerPosition.java %%JAVAJARDIR%%/bbmap/jasper/KmerPosition3.class %%JAVAJARDIR%%/bbmap/jasper/KmerPosition3.java -%%JAVAJARDIR%%/bbmap/jasper/NCBIComparison.class -%%JAVAJARDIR%%/bbmap/jasper/NCBIComparison.java -%%JAVAJARDIR%%/bbmap/jasper/NCBISparseSimilarityMatrix.class -%%JAVAJARDIR%%/bbmap/jasper/NCBISparseSimilarityMatrix.java -%%JAVAJARDIR%%/bbmap/jasper/NCBISparseTree.class -%%JAVAJARDIR%%/bbmap/jasper/NCBISparseTree.java -%%JAVAJARDIR%%/bbmap/jasper/NCBISparseTreeValidate.class -%%JAVAJARDIR%%/bbmap/jasper/NCBISparseTreeValidate.java -%%JAVAJARDIR%%/bbmap/jasper/NCBITreeNode.class -%%JAVAJARDIR%%/bbmap/jasper/NCBITreeNode.java -%%JAVAJARDIR%%/bbmap/jasper/Organism.class -%%JAVAJARDIR%%/bbmap/jasper/Organism.java -%%JAVAJARDIR%%/bbmap/jasper/SimilarityMatrix.class -%%JAVAJARDIR%%/bbmap/jasper/SimilarityMatrix.java -%%JAVAJARDIR%%/bbmap/jasper/SparseSimilarityMatrix.class -%%JAVAJARDIR%%/bbmap/jasper/SparseSimilarityMatrix.java -%%JAVAJARDIR%%/bbmap/jasper/SparseTree.class -%%JAVAJARDIR%%/bbmap/jasper/SparseTree.java -%%JAVAJARDIR%%/bbmap/jasper/SparseTreeValidate.class -%%JAVAJARDIR%%/bbmap/jasper/SparseTreeValidate.java -%%JAVAJARDIR%%/bbmap/jasper/TaxCompare.class -%%JAVAJARDIR%%/bbmap/jasper/TaxCompare.java -%%JAVAJARDIR%%/bbmap/jasper/TreeNode.class -%%JAVAJARDIR%%/bbmap/jasper/TreeNode.java +%%JAVAJARDIR%%/bbmap/jasper/README.md %%JAVAJARDIR%%/bbmap/jgi/AddAdapters.class %%JAVAJARDIR%%/bbmap/jgi/AddAdapters.java %%JAVAJARDIR%%/bbmap/jgi/AdjustHomopolymers.class %%JAVAJARDIR%%/bbmap/jgi/AdjustHomopolymers.java +%%JAVAJARDIR%%/bbmap/jgi/Assembly.class +%%JAVAJARDIR%%/bbmap/jgi/Assembly.java %%JAVAJARDIR%%/bbmap/jgi/AssemblyStats2$Triple.class %%JAVAJARDIR%%/bbmap/jgi/AssemblyStats2.class %%JAVAJARDIR%%/bbmap/jgi/AssemblyStats2.java +%%JAVAJARDIR%%/bbmap/jgi/AssemblyStats3.class +%%JAVAJARDIR%%/bbmap/jgi/AssemblyStats3.java %%JAVAJARDIR%%/bbmap/jgi/AssemblyStatsWrapper.class %%JAVAJARDIR%%/bbmap/jgi/AssemblyStatsWrapper.java %%JAVAJARDIR%%/bbmap/jgi/BBDuk$LoadThread.class @@ -1189,6 +1447,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/jgi/CheckStrand.class %%JAVAJARDIR%%/bbmap/jgi/CheckStrand.java %%JAVAJARDIR%%/bbmap/jgi/CheckStrand2$ProcessThread.class +%%JAVAJARDIR%%/bbmap/jgi/CheckStrand2$Seq.class %%JAVAJARDIR%%/bbmap/jgi/CheckStrand2.class %%JAVAJARDIR%%/bbmap/jgi/CheckStrand2.java %%JAVAJARDIR%%/bbmap/jgi/Consect.class @@ -1216,9 +1475,6 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/jgi/CrisprFinder$ProcessThread.class %%JAVAJARDIR%%/bbmap/jgi/CrisprFinder.class %%JAVAJARDIR%%/bbmap/jgi/CrisprFinder.java -%%JAVAJARDIR%%/bbmap/jgi/CrossContaminate$Vessel.class -%%JAVAJARDIR%%/bbmap/jgi/CrossContaminate.class -%%JAVAJARDIR%%/bbmap/jgi/CrossContaminate.java %%JAVAJARDIR%%/bbmap/jgi/CutPrimers.class %%JAVAJARDIR%%/bbmap/jgi/CutPrimers.java %%JAVAJARDIR%%/bbmap/jgi/DecontaminateByNormalization.class @@ -1259,8 +1515,6 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/jgi/DemuxByName2.java %%JAVAJARDIR%%/bbmap/jgi/Difference.class %%JAVAJARDIR%%/bbmap/jgi/Difference.java -%%JAVAJARDIR%%/bbmap/jgi/FakeReads.class -%%JAVAJARDIR%%/bbmap/jgi/FakeReads.java %%JAVAJARDIR%%/bbmap/jgi/FilterByCoverage.class %%JAVAJARDIR%%/bbmap/jgi/FilterByCoverage.java %%JAVAJARDIR%%/bbmap/jgi/FilterBySequence$Code.class @@ -1281,8 +1535,6 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/jgi/FindString.java %%JAVAJARDIR%%/bbmap/jgi/FungalRelease.class %%JAVAJARDIR%%/bbmap/jgi/FungalRelease.java -%%JAVAJARDIR%%/bbmap/jgi/FuseSequence.class -%%JAVAJARDIR%%/bbmap/jgi/FuseSequence.java %%JAVAJARDIR%%/bbmap/jgi/GatherKapaStats$KapaEntry.class %%JAVAJARDIR%%/bbmap/jgi/GatherKapaStats$Plate.class %%JAVAJARDIR%%/bbmap/jgi/GatherKapaStats$TagData.class @@ -1323,10 +1575,6 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/jgi/KmerNormalize.java %%JAVAJARDIR%%/bbmap/jgi/KmerSample.class %%JAVAJARDIR%%/bbmap/jgi/KmerSample.java -%%JAVAJARDIR%%/bbmap/jgi/MakeChimeras.class -%%JAVAJARDIR%%/bbmap/jgi/MakeChimeras.java -%%JAVAJARDIR%%/bbmap/jgi/MakeContaminatedGenomes.class -%%JAVAJARDIR%%/bbmap/jgi/MakeContaminatedGenomes.java %%JAVAJARDIR%%/bbmap/jgi/MakeLengthHistogram$1.class %%JAVAJARDIR%%/bbmap/jgi/MakeLengthHistogram.class %%JAVAJARDIR%%/bbmap/jgi/MakeLengthHistogram.java @@ -1336,12 +1584,6 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/jgi/MergeBarcodes.java %%JAVAJARDIR%%/bbmap/jgi/MergeSam.class %%JAVAJARDIR%%/bbmap/jgi/MergeSam.java -%%JAVAJARDIR%%/bbmap/jgi/MutateGenome$SmallVar.class -%%JAVAJARDIR%%/bbmap/jgi/MutateGenome.class -%%JAVAJARDIR%%/bbmap/jgi/MutateGenome.java -%%JAVAJARDIR%%/bbmap/jgi/MutateGenome2$SmallVar.class -%%JAVAJARDIR%%/bbmap/jgi/MutateGenome2.class -%%JAVAJARDIR%%/bbmap/jgi/MutateGenome2.java %%JAVAJARDIR%%/bbmap/jgi/Orf.class %%JAVAJARDIR%%/bbmap/jgi/Orf.java %%JAVAJARDIR%%/bbmap/jgi/PartitionReads$Partition.class @@ -1353,18 +1595,19 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/jgi/PickSubset$Node.class %%JAVAJARDIR%%/bbmap/jgi/PickSubset.class %%JAVAJARDIR%%/bbmap/jgi/PickSubset.java +%%JAVAJARDIR%%/bbmap/jgi/README.md %%JAVAJARDIR%%/bbmap/jgi/RQCFilter2.class %%JAVAJARDIR%%/bbmap/jgi/RQCFilter2.java %%JAVAJARDIR%%/bbmap/jgi/RQCFilterStats.class %%JAVAJARDIR%%/bbmap/jgi/RQCFilterStats.java -%%JAVAJARDIR%%/bbmap/jgi/RandomGenome.class -%%JAVAJARDIR%%/bbmap/jgi/RandomGenome.java %%JAVAJARDIR%%/bbmap/jgi/ReadKmerDepthDistribution$1.class %%JAVAJARDIR%%/bbmap/jgi/ReadKmerDepthDistribution$ProcessThread.class %%JAVAJARDIR%%/bbmap/jgi/ReadKmerDepthDistribution.class %%JAVAJARDIR%%/bbmap/jgi/ReadKmerDepthDistribution.java %%JAVAJARDIR%%/bbmap/jgi/RedirectTest.class %%JAVAJARDIR%%/bbmap/jgi/RedirectTest.java +%%JAVAJARDIR%%/bbmap/jgi/RefRenamer.class +%%JAVAJARDIR%%/bbmap/jgi/RefRenamer.java %%JAVAJARDIR%%/bbmap/jgi/ReformatReads.class %%JAVAJARDIR%%/bbmap/jgi/ReformatReads.java %%JAVAJARDIR%%/bbmap/jgi/RemapQuality.class @@ -1389,8 +1632,6 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/jgi/Seal.java %%JAVAJARDIR%%/bbmap/jgi/SealRefInfo.class %%JAVAJARDIR%%/bbmap/jgi/SealRefInfo.java -%%JAVAJARDIR%%/bbmap/jgi/Shred.class -%%JAVAJARDIR%%/bbmap/jgi/Shred.java %%JAVAJARDIR%%/bbmap/jgi/SmallKmerFrequency$CountComparator.class %%JAVAJARDIR%%/bbmap/jgi/SmallKmerFrequency$Kmer.class %%JAVAJARDIR%%/bbmap/jgi/SmallKmerFrequency$NumComparator.class @@ -1406,8 +1647,6 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/jgi/SplitSam6Way.java %%JAVAJARDIR%%/bbmap/jgi/SplitSamFile.class %%JAVAJARDIR%%/bbmap/jgi/SplitSamFile.java -%%JAVAJARDIR%%/bbmap/jgi/SynthMDA.class -%%JAVAJARDIR%%/bbmap/jgi/SynthMDA.java %%JAVAJARDIR%%/bbmap/jgi/TestFilesystem$WriteThread.class %%JAVAJARDIR%%/bbmap/jgi/TestFilesystem.class %%JAVAJARDIR%%/bbmap/jgi/TestFilesystem.java @@ -1418,6 +1657,10 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/jgi/TetramerFrequencies$PrintThread.class %%JAVAJARDIR%%/bbmap/jgi/TetramerFrequencies.class %%JAVAJARDIR%%/bbmap/jgi/TetramerFrequencies.java +%%JAVAJARDIR%%/bbmap/jgi/TetramerFrequencies_old$Line.class +%%JAVAJARDIR%%/bbmap/jgi/TetramerFrequencies_old$PrintThread.class +%%JAVAJARDIR%%/bbmap/jgi/TetramerFrequencies_old.class +%%JAVAJARDIR%%/bbmap/jgi/TetramerFrequencies_old.java %%JAVAJARDIR%%/bbmap/jgi/TranslateSixFrames.class %%JAVAJARDIR%%/bbmap/jgi/TranslateSixFrames.java %%JAVAJARDIR%%/bbmap/jgi/TrimContigs$Range.class @@ -1433,6 +1676,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/json/JsonObject.java %%JAVAJARDIR%%/bbmap/json/JsonParser.class %%JAVAJARDIR%%/bbmap/json/JsonParser.java +%%JAVAJARDIR%%/bbmap/json/README.md %%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTable$AllocThread.class %%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTable.class %%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTable.java @@ -1476,6 +1720,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/kmer/KmerTableSet.java %%JAVAJARDIR%%/bbmap/kmer/OwnershipThread.class %%JAVAJARDIR%%/bbmap/kmer/OwnershipThread.java +%%JAVAJARDIR%%/bbmap/kmer/README.md %%JAVAJARDIR%%/bbmap/kmer/ScheduleMaker.class %%JAVAJARDIR%%/bbmap/kmer/ScheduleMaker.java %%JAVAJARDIR%%/bbmap/kmer/SimpleKmerTable.class @@ -1497,7 +1742,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/ml/CellNetParser.java %%JAVAJARDIR%%/bbmap/ml/CellNetReverseComparator.class %%JAVAJARDIR%%/bbmap/ml/CellNetReverseComparator.java -%%JAVAJARDIR%%/bbmap/ml/DataLoader$Pair.class +%%JAVAJARDIR%%/bbmap/ml/DataLoader$Triple.class %%JAVAJARDIR%%/bbmap/ml/DataLoader.class %%JAVAJARDIR%%/bbmap/ml/DataLoader.java %%JAVAJARDIR%%/bbmap/ml/ExtendedMSig.class @@ -1524,8 +1769,11 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/ml/ProcessBBMergeHeaders.java %%JAVAJARDIR%%/bbmap/ml/Profiler.class %%JAVAJARDIR%%/bbmap/ml/Profiler.java +%%JAVAJARDIR%%/bbmap/ml/README.md %%JAVAJARDIR%%/bbmap/ml/RSLog.class %%JAVAJARDIR%%/bbmap/ml/RSLog.java +%%JAVAJARDIR%%/bbmap/ml/ReduceColumns.class +%%JAVAJARDIR%%/bbmap/ml/ReduceColumns.java %%JAVAJARDIR%%/bbmap/ml/Sample.class %%JAVAJARDIR%%/bbmap/ml/Sample.java %%JAVAJARDIR%%/bbmap/ml/SampleErrorComparator.class @@ -1586,6 +1834,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/pacbio/ProcessStackedSitesNormalized$Ssra.class %%JAVAJARDIR%%/bbmap/pacbio/ProcessStackedSitesNormalized.class %%JAVAJARDIR%%/bbmap/pacbio/ProcessStackedSitesNormalized.java +%%JAVAJARDIR%%/bbmap/pacbio/README.md %%JAVAJARDIR%%/bbmap/pacbio/RemoveAdapters2$1.class %%JAVAJARDIR%%/bbmap/pacbio/RemoveAdapters2$ProcessThread.class %%JAVAJARDIR%%/bbmap/pacbio/RemoveAdapters2.class @@ -1648,6 +1897,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/prok/PGMTools.java %%JAVAJARDIR%%/bbmap/prok/ProkObject.class %%JAVAJARDIR%%/bbmap/prok/ProkObject.java +%%JAVAJARDIR%%/bbmap/prok/README.md %%JAVAJARDIR%%/bbmap/prok/RiboMaker$ProcessThread.class %%JAVAJARDIR%%/bbmap/prok/RiboMaker.class %%JAVAJARDIR%%/bbmap/prok/RiboMaker.java @@ -1675,14 +1925,30 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/repeat/RepeatSet.java %%JAVAJARDIR%%/bbmap/server/PercentEncoding.class %%JAVAJARDIR%%/bbmap/server/PercentEncoding.java +%%JAVAJARDIR%%/bbmap/server/README.md %%JAVAJARDIR%%/bbmap/server/ServerTools$1.class %%JAVAJARDIR%%/bbmap/server/ServerTools.class %%JAVAJARDIR%%/bbmap/server/ServerTools.java %%JAVAJARDIR%%/bbmap/server/SimpleHttpServer$GetHandler.class %%JAVAJARDIR%%/bbmap/server/SimpleHttpServer.class %%JAVAJARDIR%%/bbmap/server/SimpleHttpServer.java +%%JAVAJARDIR%%/bbmap/server/StressTest.class +%%JAVAJARDIR%%/bbmap/server/StressTest.java +%%JAVAJARDIR%%/bbmap/server/StressTest2$1.class +%%JAVAJARDIR%%/bbmap/server/StressTest2.class +%%JAVAJARDIR%%/bbmap/server/StressTest2.java +%%JAVAJARDIR%%/bbmap/server/StressTest3.class +%%JAVAJARDIR%%/bbmap/server/StressTest3.java %%JAVAJARDIR%%/bbmap/shared/Colors.class %%JAVAJARDIR%%/bbmap/shared/Colors.java +%%JAVAJARDIR%%/bbmap/shared/FastRandom.class +%%JAVAJARDIR%%/bbmap/shared/FastRandom.java +%%JAVAJARDIR%%/bbmap/shared/FastRandomAES.class +%%JAVAJARDIR%%/bbmap/shared/FastRandomAES.java +%%JAVAJARDIR%%/bbmap/shared/FastRandomSIMD.class +%%JAVAJARDIR%%/bbmap/shared/FastRandomSIMD.java +%%JAVAJARDIR%%/bbmap/shared/FastRandomXoshiro.class +%%JAVAJARDIR%%/bbmap/shared/FastRandomXoshiro.java %%JAVAJARDIR%%/bbmap/shared/KillSwitch.class %%JAVAJARDIR%%/bbmap/shared/KillSwitch.java %%JAVAJARDIR%%/bbmap/shared/LineParser.class @@ -1717,10 +1983,19 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/shared/PreParser.java %%JAVAJARDIR%%/bbmap/shared/Primes.class %%JAVAJARDIR%%/bbmap/shared/Primes.java +%%JAVAJARDIR%%/bbmap/shared/README.md %%JAVAJARDIR%%/bbmap/shared/SIMD.class %%JAVAJARDIR%%/bbmap/shared/SIMD.java +%%JAVAJARDIR%%/bbmap/shared/SIMDAlign.class +%%JAVAJARDIR%%/bbmap/shared/SIMDAlign.java +%%JAVAJARDIR%%/bbmap/shared/SIMDAlignByte.class +%%JAVAJARDIR%%/bbmap/shared/SIMDAlignByte.java +%%JAVAJARDIR%%/bbmap/shared/SIMDAlignOld.class +%%JAVAJARDIR%%/bbmap/shared/SIMDAlignOld.java %%JAVAJARDIR%%/bbmap/shared/Shared.class %%JAVAJARDIR%%/bbmap/shared/Shared.java +%%JAVAJARDIR%%/bbmap/shared/SyncHeart.class +%%JAVAJARDIR%%/bbmap/shared/SyncHeart.java %%JAVAJARDIR%%/bbmap/shared/Timer.class %%JAVAJARDIR%%/bbmap/shared/Timer.java %%JAVAJARDIR%%/bbmap/shared/Tools$1.class @@ -1770,8 +2045,6 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/sketch/Comparison.java %%JAVAJARDIR%%/bbmap/sketch/DisplayParams.class %%JAVAJARDIR%%/bbmap/sketch/DisplayParams.java -%%JAVAJARDIR%%/bbmap/sketch/GlocalAligner.class -%%JAVAJARDIR%%/bbmap/sketch/GlocalAligner.java %%JAVAJARDIR%%/bbmap/sketch/InvertKey.class %%JAVAJARDIR%%/bbmap/sketch/InvertKey.java %%JAVAJARDIR%%/bbmap/sketch/KmerLimit$ProcessThread.class @@ -1782,6 +2055,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/sketch/KmerLimit2.java %%JAVAJARDIR%%/bbmap/sketch/MergeSketch.class %%JAVAJARDIR%%/bbmap/sketch/MergeSketch.java +%%JAVAJARDIR%%/bbmap/sketch/README.md %%JAVAJARDIR%%/bbmap/sketch/Record.class %%JAVAJARDIR%%/bbmap/sketch/Record.java %%JAVAJARDIR%%/bbmap/sketch/RecordSet.class @@ -1831,6 +2105,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/sort/ContigLengthComparator.java %%JAVAJARDIR%%/bbmap/sort/MergeSorted.class %%JAVAJARDIR%%/bbmap/sort/MergeSorted.java +%%JAVAJARDIR%%/bbmap/sort/README.md %%JAVAJARDIR%%/bbmap/sort/ReadComparator.class %%JAVAJARDIR%%/bbmap/sort/ReadComparator.java %%JAVAJARDIR%%/bbmap/sort/ReadComparatorClump.class @@ -2053,6 +2328,8 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/structures/IntList3.java %%JAVAJARDIR%%/bbmap/structures/IntListCompressor.class %%JAVAJARDIR%%/bbmap/structures/IntListCompressor.java +%%JAVAJARDIR%%/bbmap/structures/IntListHashMap.class +%%JAVAJARDIR%%/bbmap/structures/IntListHashMap.java %%JAVAJARDIR%%/bbmap/structures/IntLongHashMap.class %%JAVAJARDIR%%/bbmap/structures/IntLongHashMap.java %%JAVAJARDIR%%/bbmap/structures/IntMap.class @@ -2098,10 +2375,17 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/structures/Point.java %%JAVAJARDIR%%/bbmap/structures/Quantizer.class %%JAVAJARDIR%%/bbmap/structures/Quantizer.java +%%JAVAJARDIR%%/bbmap/structures/README.md %%JAVAJARDIR%%/bbmap/structures/Range.class %%JAVAJARDIR%%/bbmap/structures/Range.java %%JAVAJARDIR%%/bbmap/structures/RawBitSet.class %%JAVAJARDIR%%/bbmap/structures/RawBitSet.java +%%JAVAJARDIR%%/bbmap/structures/RingBuffer.class +%%JAVAJARDIR%%/bbmap/structures/RingBuffer.java +%%JAVAJARDIR%%/bbmap/structures/RingBufferMask.class +%%JAVAJARDIR%%/bbmap/structures/RingBufferMask.java +%%JAVAJARDIR%%/bbmap/structures/RingBufferMod.class +%%JAVAJARDIR%%/bbmap/structures/RingBufferMod.java %%JAVAJARDIR%%/bbmap/structures/SeqCount.class %%JAVAJARDIR%%/bbmap/structures/SeqCount.java %%JAVAJARDIR%%/bbmap/structures/SeqCountM.class @@ -2128,6 +2412,41 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/structures/StringPair.java %%JAVAJARDIR%%/bbmap/structures/SuperLongList.class %%JAVAJARDIR%%/bbmap/structures/SuperLongList.java +%%JAVAJARDIR%%/bbmap/synth/CoverageModel.class +%%JAVAJARDIR%%/bbmap/synth/CoverageModel.java +%%JAVAJARDIR%%/bbmap/synth/CrossContaminate$Vessel.class +%%JAVAJARDIR%%/bbmap/synth/CrossContaminate.class +%%JAVAJARDIR%%/bbmap/synth/CrossContaminate.java +%%JAVAJARDIR%%/bbmap/synth/FakeReads.class +%%JAVAJARDIR%%/bbmap/synth/FakeReads.java +%%JAVAJARDIR%%/bbmap/synth/FuseSequence.class +%%JAVAJARDIR%%/bbmap/synth/FuseSequence.java +%%JAVAJARDIR%%/bbmap/synth/GCBias.class +%%JAVAJARDIR%%/bbmap/synth/GCBias.java +%%JAVAJARDIR%%/bbmap/synth/MakeChimeras.class +%%JAVAJARDIR%%/bbmap/synth/MakeChimeras.java +%%JAVAJARDIR%%/bbmap/synth/MakeContaminatedGenomes.class +%%JAVAJARDIR%%/bbmap/synth/MakeContaminatedGenomes.java +%%JAVAJARDIR%%/bbmap/synth/MutateGenome$SmallVar.class +%%JAVAJARDIR%%/bbmap/synth/MutateGenome.class +%%JAVAJARDIR%%/bbmap/synth/MutateGenome.java +%%JAVAJARDIR%%/bbmap/synth/MutateGenome2$SmallVar.class +%%JAVAJARDIR%%/bbmap/synth/MutateGenome2.class +%%JAVAJARDIR%%/bbmap/synth/MutateGenome2.java +%%JAVAJARDIR%%/bbmap/synth/RandomGenome.class +%%JAVAJARDIR%%/bbmap/synth/RandomGenome.java +%%JAVAJARDIR%%/bbmap/synth/RandomHexamer.class +%%JAVAJARDIR%%/bbmap/synth/RandomHexamer.java +%%JAVAJARDIR%%/bbmap/synth/RandomReads3$1.class +%%JAVAJARDIR%%/bbmap/synth/RandomReads3.class +%%JAVAJARDIR%%/bbmap/synth/RandomReads3.java +%%JAVAJARDIR%%/bbmap/synth/RandomReadsMG$ProcessThread.class +%%JAVAJARDIR%%/bbmap/synth/RandomReadsMG.class +%%JAVAJARDIR%%/bbmap/synth/RandomReadsMG.java +%%JAVAJARDIR%%/bbmap/synth/Shred.class +%%JAVAJARDIR%%/bbmap/synth/Shred.java +%%JAVAJARDIR%%/bbmap/synth/SynthMDA.class +%%JAVAJARDIR%%/bbmap/synth/SynthMDA.java %%JAVAJARDIR%%/bbmap/tax/AccessionToTaxid$HashThread.class %%JAVAJARDIR%%/bbmap/tax/AccessionToTaxid.class %%JAVAJARDIR%%/bbmap/tax/AccessionToTaxid.java @@ -2139,6 +2458,8 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/tax/AnalyzeAccession.java %%JAVAJARDIR%%/bbmap/tax/AnalyzeAccession_ST.class %%JAVAJARDIR%%/bbmap/tax/AnalyzeAccession_ST.java +%%JAVAJARDIR%%/bbmap/tax/CanonicalLineage.class +%%JAVAJARDIR%%/bbmap/tax/CanonicalLineage.java %%JAVAJARDIR%%/bbmap/tax/ExplodeTree.class %%JAVAJARDIR%%/bbmap/tax/ExplodeTree.java %%JAVAJARDIR%%/bbmap/tax/FilterByTaxa.class @@ -2157,10 +2478,13 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/tax/ImgRecord.java %%JAVAJARDIR%%/bbmap/tax/ImgRecord2.class %%JAVAJARDIR%%/bbmap/tax/ImgRecord2.java +%%JAVAJARDIR%%/bbmap/tax/Lineage.class +%%JAVAJARDIR%%/bbmap/tax/Lineage.java %%JAVAJARDIR%%/bbmap/tax/PrintTaxonomy.class %%JAVAJARDIR%%/bbmap/tax/PrintTaxonomy.java %%JAVAJARDIR%%/bbmap/tax/Query.class %%JAVAJARDIR%%/bbmap/tax/Query.java +%%JAVAJARDIR%%/bbmap/tax/README.md %%JAVAJARDIR%%/bbmap/tax/RenameGiToTaxid.class %%JAVAJARDIR%%/bbmap/tax/RenameGiToTaxid.java %%JAVAJARDIR%%/bbmap/tax/RenameIMG.class @@ -2230,6 +2554,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/template/BBTool_ST.java %%JAVAJARDIR%%/bbmap/template/DoWorker.class %%JAVAJARDIR%%/bbmap/template/DoWorker.java +%%JAVAJARDIR%%/bbmap/template/README.md %%JAVAJARDIR%%/bbmap/template/ThreadPoolJob.class %%JAVAJARDIR%%/bbmap/template/ThreadPoolJob.java %%JAVAJARDIR%%/bbmap/template/ThreadWaiter.class @@ -2288,6 +2613,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/ukmer/KmerTableSetU.java %%JAVAJARDIR%%/bbmap/ukmer/OwnershipThread.class %%JAVAJARDIR%%/bbmap/ukmer/OwnershipThread.java +%%JAVAJARDIR%%/bbmap/ukmer/README.md %%JAVAJARDIR%%/bbmap/ukmer/WalkerU.class %%JAVAJARDIR%%/bbmap/ukmer/WalkerU.java %%JAVAJARDIR%%/bbmap/var/ApplyVarsToReference$1.class @@ -2307,6 +2633,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/var/GenerateVarlets3$ProcessThread.class %%JAVAJARDIR%%/bbmap/var/GenerateVarlets3.class %%JAVAJARDIR%%/bbmap/var/GenerateVarlets3.java +%%JAVAJARDIR%%/bbmap/var/README.md %%JAVAJARDIR%%/bbmap/var/StackVariations$1.class %%JAVAJARDIR%%/bbmap/var/StackVariations$SVThread.class %%JAVAJARDIR%%/bbmap/var/StackVariations.class @@ -2321,8 +2648,12 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/var/Variation.java %%JAVAJARDIR%%/bbmap/var/Varlet.class %%JAVAJARDIR%%/bbmap/var/Varlet.java +%%JAVAJARDIR%%/bbmap/var2/AnalyzeVars.class +%%JAVAJARDIR%%/bbmap/var2/AnalyzeVars.java %%JAVAJARDIR%%/bbmap/var2/ApplyVariants.class %%JAVAJARDIR%%/bbmap/var2/ApplyVariants.java +%%JAVAJARDIR%%/bbmap/var2/CVOutputWriter.class +%%JAVAJARDIR%%/bbmap/var2/CVOutputWriter.java %%JAVAJARDIR%%/bbmap/var2/CallVariants$ProcessThread.class %%JAVAJARDIR%%/bbmap/var2/CallVariants.class %%JAVAJARDIR%%/bbmap/var2/CallVariants.java @@ -2332,6 +2663,8 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/var2/CallVariants2.java %%JAVAJARDIR%%/bbmap/var2/CompareVCF.class %%JAVAJARDIR%%/bbmap/var2/CompareVCF.java +%%JAVAJARDIR%%/bbmap/var2/FeatureVectorMaker.class +%%JAVAJARDIR%%/bbmap/var2/FeatureVectorMaker.java %%JAVAJARDIR%%/bbmap/var2/FilterSam$ProcessThread.class %%JAVAJARDIR%%/bbmap/var2/FilterSam.class %%JAVAJARDIR%%/bbmap/var2/FilterSam.java @@ -2341,6 +2674,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/var2/MergeSamples$MergeThread.class %%JAVAJARDIR%%/bbmap/var2/MergeSamples.class %%JAVAJARDIR%%/bbmap/var2/MergeSamples.java +%%JAVAJARDIR%%/bbmap/var2/README.md %%JAVAJARDIR%%/bbmap/var2/Realign$ProcessThread.class %%JAVAJARDIR%%/bbmap/var2/Realign.class %%JAVAJARDIR%%/bbmap/var2/Realign.java @@ -2363,15 +2697,27 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/var2/Var.java %%JAVAJARDIR%%/bbmap/var2/VarFilter.class %%JAVAJARDIR%%/bbmap/var2/VarFilter.java +%%JAVAJARDIR%%/bbmap/var2/VarHelper.class +%%JAVAJARDIR%%/bbmap/var2/VarHelper.java %%JAVAJARDIR%%/bbmap/var2/VarKey.class %%JAVAJARDIR%%/bbmap/var2/VarKey.java %%JAVAJARDIR%%/bbmap/var2/VarMap$ProcessThread.class %%JAVAJARDIR%%/bbmap/var2/VarMap$VarMapIterator.class %%JAVAJARDIR%%/bbmap/var2/VarMap.class %%JAVAJARDIR%%/bbmap/var2/VarMap.java +%%JAVAJARDIR%%/bbmap/var2/VarProb.class +%%JAVAJARDIR%%/bbmap/var2/VarProb.java %%JAVAJARDIR%%/bbmap/var2/VcfLoader$ProcessThread.class %%JAVAJARDIR%%/bbmap/var2/VcfLoader.class %%JAVAJARDIR%%/bbmap/var2/VcfLoader.java +%%JAVAJARDIR%%/bbmap/var2/VcfToVar.class +%%JAVAJARDIR%%/bbmap/var2/VcfToVar.java %%JAVAJARDIR%%/bbmap/var2/VcfWriter$ProcessThread.class %%JAVAJARDIR%%/bbmap/var2/VcfWriter.class %%JAVAJARDIR%%/bbmap/var2/VcfWriter.java +%%JAVAJARDIR%%/bbmap/var2/VectorDonovan$QuantileTransformer.class +%%JAVAJARDIR%%/bbmap/var2/VectorDonovan.class +%%JAVAJARDIR%%/bbmap/var2/VectorDonovan.java +%%JAVAJARDIR%%/bbmap/var2/VectorElba$ElbaMinMaxValues.class +%%JAVAJARDIR%%/bbmap/var2/VectorElba.class +%%JAVAJARDIR%%/bbmap/var2/VectorElba.java diff --git a/biology/bcf-score/Makefile b/biology/bcf-score/Makefile index bd2d2610e27e..dc846f339fad 100644 --- a/biology/bcf-score/Makefile +++ b/biology/bcf-score/Makefile @@ -1,6 +1,6 @@ PORTNAME= bcf-score DISTVERSION= 1.20 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= biology MASTER_SITES= https://software.broadinstitute.org/software/score/ # Get this right, or ports will download bcftools in it's place via tuple diff --git a/biology/biococoa/Makefile b/biology/biococoa/Makefile index 56145db6d6be..84b6d7f8d722 100644 --- a/biology/biococoa/Makefile +++ b/biology/biococoa/Makefile @@ -1,6 +1,6 @@ PORTNAME= biococoa PORTVERSION= 2.2.2 -PORTREVISION= 8 +PORTREVISION= 9 CATEGORIES= biology gnustep MASTER_SITES= http://bioinformatics.org/biococoa/downloads/ DISTNAME= biococoa-${PORTVERSION}-src diff --git a/biology/biosig/Makefile b/biology/biosig/Makefile index 1a676735a7d6..5bfc428dd205 100644 --- a/biology/biosig/Makefile +++ b/biology/biosig/Makefile @@ -1,6 +1,6 @@ PORTNAME= biosig DISTVERSION= 2.6.1 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= biology MASTER_SITES= SF/${PORTNAME}/BioSig%20for%20C_C%2B%2B/src/ DISTNAME= ${PORTNAME}-${PORTVERSION}.src diff --git a/biology/bwa/Makefile b/biology/bwa/Makefile index 3481077c3af3..eacf6225f663 100644 --- a/biology/bwa/Makefile +++ b/biology/bwa/Makefile @@ -3,7 +3,7 @@ DISTVERSIONPREFIX= v DISTVERSION= 0.7.19 CATEGORIES= biology -MAINTAINER= alster@vinterdalen.se +MAINTAINER= alven@FreeBSD.org COMMENT= Burrows-Wheeler sequence aligner WWW= https://bio-bwa.sourceforge.net/ \ https://sourceforge.net/projects/bio-bwa/ \ diff --git a/biology/diamond/Makefile b/biology/diamond/Makefile index aef831bfd9c2..7884486cf917 100644 --- a/biology/diamond/Makefile +++ b/biology/diamond/Makefile @@ -1,6 +1,6 @@ PORTNAME= diamond DISTVERSIONPREFIX= v -DISTVERSION= 2.1.11 +DISTVERSION= 2.1.13 CATEGORIES= biology MAINTAINER= jrm@FreeBSD.org diff --git a/biology/diamond/distinfo b/biology/diamond/distinfo index bd79b1dbc15f..c2a537bdb17a 100644 --- a/biology/diamond/distinfo +++ b/biology/diamond/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1737814516 -SHA256 (bbuchfink-diamond-v2.1.11_GH0.tar.gz) = e669e74ac4a7e45d86024a6b9bfda0642fabb02a8b6ce90a2ec7fb3aeb0f8233 -SIZE (bbuchfink-diamond-v2.1.11_GH0.tar.gz) = 5934620 +TIMESTAMP = 1755281950 +SHA256 (bbuchfink-diamond-v2.1.13_GH0.tar.gz) = d3d093b77d0ad8914f3e94dc53b9b2684cb77990765e1a2fe93ad022c28930f5 +SIZE (bbuchfink-diamond-v2.1.13_GH0.tar.gz) = 5953400 diff --git a/biology/gatk/Makefile b/biology/gatk/Makefile index 41df894298f4..49a990d3f216 100644 --- a/biology/gatk/Makefile +++ b/biology/gatk/Makefile @@ -1,6 +1,5 @@ PORTNAME= gatk -DISTVERSION= 4.6.1.0 -PORTREVISION= 1 +DISTVERSION= 4.6.2.0 CATEGORIES= biology java EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} @@ -31,7 +30,7 @@ NO_ARCH= yes DEPS_CACHE_DIR= ${WRKDIR} TEST_ENV= ${MAKE_ENV} \ - JAVA_TOOL_OPTIONS="-DLIBBWA_PATH=${PREFIX}/lib/libfml.so" \ + JAVA_TOOL_OPTIONS="-DLIBBWA_PATH=${PREFIX}/lib/libfml.so -DLIBFML_PATH=${PREFIX}/lib/libfml.so" \ GATK_LOCAL_JAR=${STAGEDIR}${JAVAJARDIR}/GenomeAnalysisTK-${PORTVERSION}.jar PLIST_FILES= bin/${PORTNAME} \ @@ -117,9 +116,10 @@ do-install: do-test: # tests require WITH_LARGE_FILES=ON, and they use a lot of disk space @cd ${WRKSRC} && \ - ${SETENV} ${TEST_ENV} gradle8 -DLIBBWA_PATH=${PREFIX}/lib/libfml.so test + ${SETENV} ${TEST_ENV} gradle8 test -# tests results as of version 4.6.1.0: 288552 tests, 301 failures, 37 ignored, 1h55m5.63s duration, 99% successful, see https://github.com/broadinstitute/gatk/issues/8940 +# tests as of 4.6.1.0: 288552 tests, 301 failures, 37 ignored, 1h55m5.63s duration, 99% successful, see https://github.com/broadinstitute/gatk/issues/8940 +# tests as of 4.6.2.0: 288719 tests completed, 300 failed, 37 skipped # see https://github.com/broadinstitute/gatk/issues/8939: Tests fail to find libgkl libraries in /usr/local/lib .include <bsd.port.mk> diff --git a/biology/gatk/distinfo b/biology/gatk/distinfo index 2494dc43dd72..42fbad5e8a91 100644 --- a/biology/gatk/distinfo +++ b/biology/gatk/distinfo @@ -1,5 +1,5 @@ -TIMESTAMP = 1730356703 -SHA256 (gatk-4.6.1.0-deps.tar.gz) = ea0205776f26bbe51bcdea6dd10df975a2e4861a772901523ff7ab123119b8ad -SIZE (gatk-4.6.1.0-deps.tar.gz) = 922113997 -SHA256 (broadinstitute-gatk-4.6.1.0_GH0.tar.gz) = 6f840406ce226e202421464e2ae044f3c0bc63da63f245568f8ca1bc7769d378 -SIZE (broadinstitute-gatk-4.6.1.0_GH0.tar.gz) = 4317548196 +TIMESTAMP = 1756227460 +SHA256 (gatk-4.6.2.0-deps.tar.gz) = c956ec3b6a209b4eaf9c20cb312635498b360aa372f824b33d392aa0ac594a77 +SIZE (gatk-4.6.2.0-deps.tar.gz) = 903933113 +SHA256 (broadinstitute-gatk-4.6.2.0_GH0.tar.gz) = c76b61a549f49004a54ae86e88cd8b7a180a3bd2e4a56b1c9185f30971c79866 +SIZE (broadinstitute-gatk-4.6.2.0_GH0.tar.gz) = 4318674606 diff --git a/biology/gatk/files/gatk.sh.in b/biology/gatk/files/gatk.sh.in index d3d5c0f7bf5a..20c6c16d5164 100644 --- a/biology/gatk/files/gatk.sh.in +++ b/biology/gatk/files/gatk.sh.in @@ -23,5 +23,5 @@ fi # execute the command # add the LIBBWA_PATH system parameter (not sure whether the env. var or argument alone are sufficient) -JAVA_TOOL_OPTIONS="-DLIBBWA_PATH=%%PREFIX%%/lib/libfml.so" \ -%%JAVA%% $MEM_OPTS -DLIBBWA_PATH=%%PREFIX%%/lib/libfml.so -jar %%JAVAJARDIR%%/GenomeAnalysisTK-%%PORTVERSION%%.jar "$@" +JAVA_TOOL_OPTIONS="-DLIBBWA_PATH=%%PREFIX%%/lib/libfml.so -DLIBFML_PATH=%%PREFIX%%/lib/libfml.so" \ +%%JAVA%% $MEM_OPTS -DLIBBWA_PATH=%%PREFIX%%/lib/libfml.so -DLIBFML_PATH=%%PREFIX%%/lib/libfml.so -jar %%JAVAJARDIR%%/GenomeAnalysisTK-%%PORTVERSION%%.jar "$@" diff --git a/biology/gkl/Makefile b/biology/gkl/Makefile index 7c4c025158c6..128a190d5839 100644 --- a/biology/gkl/Makefile +++ b/biology/gkl/Makefile @@ -1,6 +1,5 @@ PORTNAME= gkl -DISTVERSION= 0.8.11-9 -DISTVERSIONSUFFIX= -g25670d8 +DISTVERSION= 0.9.1 CATEGORIES= biology devel MAINTAINER= yuri@FreeBSD.org diff --git a/biology/gkl/distinfo b/biology/gkl/distinfo index 35c01c063547..d1758a9bcd7a 100644 --- a/biology/gkl/distinfo +++ b/biology/gkl/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1722788727 -SHA256 (Intel-HLS-GKL-0.8.11-9-g25670d8_GH0.tar.gz) = 743d1eb48c2629454a6dcb98d9adca3aaedfe9c658e6f89e890b03b6e029df61 -SIZE (Intel-HLS-GKL-0.8.11-9-g25670d8_GH0.tar.gz) = 5310668 +TIMESTAMP = 1755972512 +SHA256 (Intel-HLS-GKL-0.9.1_GH0.tar.gz) = 8e32bc3c63013ca6468c65fbbb6af80a433652b640be868d0cb82cb70a919799 +SIZE (Intel-HLS-GKL-0.9.1_GH0.tar.gz) = 5363673 diff --git a/biology/gkl/files/patch-CMakeLists.txt b/biology/gkl/files/patch-CMakeLists.txt index 2cda423767df..a05193ec57f9 100644 --- a/biology/gkl/files/patch-CMakeLists.txt +++ b/biology/gkl/files/patch-CMakeLists.txt @@ -1,6 +1,6 @@ ---- CMakeLists.txt.orig 2024-08-04 17:44:32 UTC +--- CMakeLists.txt.orig 2025-07-07 07:42:12 UTC +++ CMakeLists.txt -@@ -24,6 +24,8 @@ set(NATIVE_DIR ${PROJECT_SOURCE_DIR}/src/main/native) +@@ -28,6 +28,8 @@ set(NATIVE_DIR ${PROJECT_SOURCE_DIR}/src/main/native) # add CMakeLists.txt in subdirectories set(NATIVE_DIR ${PROJECT_SOURCE_DIR}/src/main/native) diff --git a/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm-implementation.h b/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm-implementation.h new file mode 100644 index 000000000000..b47595807911 --- /dev/null +++ b/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm-implementation.h @@ -0,0 +1,11 @@ +--- src/main/native/pdhmm/pdhmm-implementation.h.orig 2025-08-23 18:25:35 UTC ++++ src/main/native/pdhmm/pdhmm-implementation.h +@@ -31,7 +31,7 @@ + #include "avx512_impl.h" + #endif + +-#if defined(__linux__) ++#if defined(__linux__) || defined(__FreeBSD__) + #include <omp.h> + #endif + diff --git a/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm-serial.cc b/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm-serial.cc new file mode 100644 index 000000000000..ebe9e8d41887 --- /dev/null +++ b/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm-serial.cc @@ -0,0 +1,11 @@ +--- src/main/native/pdhmm/pdhmm-serial.cc.orig 2025-08-23 18:12:32 UTC ++++ src/main/native/pdhmm/pdhmm-serial.cc +@@ -24,7 +24,7 @@ + #include "pdhmm-serial.h" + #include "MathUtils.h" + #include <cstdio> +-#if defined(__linux__) ++#if defined(__linux__) || defined(__FreeBSD__) + #include <omp.h> + #endif + diff --git a/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm.h b/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm.h index 4896be46607f..b4afa8fb6791 100644 --- a/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm.h +++ b/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm.h @@ -1,4 +1,4 @@ ---- src/main/native/pdhmm/pdhmm.h.orig 2024-08-04 16:31:53 UTC +--- src/main/native/pdhmm/pdhmm.h.orig 2025-07-07 07:42:12 UTC +++ src/main/native/pdhmm/pdhmm.h @@ -27,6 +27,9 @@ #ifdef linux @@ -8,5 +8,5 @@ +#include <omp.h> +#endif - inline INT_TYPE roundDownToNearestMultipleOf(INT_TYPE val, INT_TYPE mul) { return (val / mul) * mul; } + inline INT_TYPE CONCAT(roundDownToNearestMultipleOf_, SIMD_ENGINE)(INT_TYPE val, INT_TYPE mul) { return (val / mul) * mul; } diff --git a/biology/htslib/Makefile b/biology/htslib/Makefile index 38ef7358c154..5b3c5908f428 100644 --- a/biology/htslib/Makefile +++ b/biology/htslib/Makefile @@ -15,7 +15,7 @@ LICENSE_FILE= ${WRKSRC}/LICENSE LIB_DEPENDS= libdeflate.so:archivers/libdeflate TEST_DEPENDS= bash:shells/bash -USES= autoreconf cpe gmake localbase:ldflags pathfix perl5 shebangfix tar:bzip2 +USES= autoreconf cpe gmake localbase:ldflags perl5 shebangfix tar:bzip2 USE_PERL5= test USE_LDCONFIG= yes diff --git a/biology/hyphy/Makefile b/biology/hyphy/Makefile index f281649f9c47..0e827bd9239e 100644 --- a/biology/hyphy/Makefile +++ b/biology/hyphy/Makefile @@ -1,5 +1,6 @@ PORTNAME= hyphy -DISTVERSION= 2.5.73 +DISTVERSION= 2.5.77 +PORTREVISION= 1 CATEGORIES= biology MAINTAINER= jrm@FreeBSD.org @@ -20,9 +21,11 @@ USES= cmake:insource,testing localbase:ldflags # tests fail in outsource build, USE_GITHUB= yes GH_ACCOUNT= veg -OPTIONS_DEFINE= AVX -AVX_DESC= Advanced vector extensions support +OPTIONS_DEFINE= AVX TARGET_NATIVE +AVX_DESC= Advanced vector extensions support +TARGET_NATIVE_DESC= Enable CPU-specific instructions and tuning for build machine -AVX_CMAKE_BOOL_OFF= NOAVX +AVX_CMAKE_BOOL_OFF= NOAVX +TARGET_NATIVE_CMAKE_BOOL= TARGET_NATIVE .include <bsd.port.mk> diff --git a/biology/hyphy/distinfo b/biology/hyphy/distinfo index ae85017d004d..7a055e3a0004 100644 --- a/biology/hyphy/distinfo +++ b/biology/hyphy/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1747240205 -SHA256 (veg-hyphy-2.5.73_GH0.tar.gz) = efc64adb9f270aa6c284dbee22a16132f4e59126e9df071c5267cd79e2883969 -SIZE (veg-hyphy-2.5.73_GH0.tar.gz) = 4161304 +TIMESTAMP = 1755447505 +SHA256 (veg-hyphy-2.5.77_GH0.tar.gz) = 5012efd40938caeb9894bbd480565f95d735840f8eac67c6e84884a347e32e76 +SIZE (veg-hyphy-2.5.77_GH0.tar.gz) = 4027226 diff --git a/biology/hyphy/files/patch-src_core_global__things.cpp b/biology/hyphy/files/patch-src_core_global__things.cpp new file mode 100644 index 000000000000..397be8520ae5 --- /dev/null +++ b/biology/hyphy/files/patch-src_core_global__things.cpp @@ -0,0 +1,20 @@ +--- src/core/global_things.cpp.orig 2025-08-22 19:21:44 UTC ++++ src/core/global_things.cpp +@@ -173,7 +173,7 @@ hyPointer MemAllocate(size_t bytes, bool zero, size_t + result = (hyPointer)zero ? calloc(bytes, 1) : malloc(bytes); + + if (result == nil) { +- HandleApplicationError(_String("Failed to allocate '") & bytes & "' bytes'", ++ HandleApplicationError(_String("Failed to allocate '") & (unsigned long)bytes & "' bytes'", + true); + } + return result; +@@ -186,7 +186,7 @@ hyPointer MemReallocate(hyPointer old_pointer, size_t + + if (result == nil) { + HandleApplicationError( +- _String("Failed to resize memory to '") & new_size & "' bytes'", true); ++ _String("Failed to resize memory to '") & (unsigned long)new_size & "' bytes'", true); + } + + return result; diff --git a/biology/hyphy/pkg-plist b/biology/hyphy/pkg-plist index cea5332c2742..a1151478347d 100644 --- a/biology/hyphy/pkg-plist +++ b/biology/hyphy/pkg-plist @@ -117,6 +117,9 @@ bin/hyphy %%DATADIR%%/TemplateBatchFiles/Distances/p_Distance_codon %%DATADIR%%/TemplateBatchFiles/F_ST.bf %%DATADIR%%/TemplateBatchFiles/FitnessAAModels.bf +%%DATADIR%%/TemplateBatchFiles/GA/MSS-selector-codon.bf +%%DATADIR%%/TemplateBatchFiles/GA/README.md +%%DATADIR%%/TemplateBatchFiles/GA/processor-codon.bf %%DATADIR%%/TemplateBatchFiles/GARD.bf %%DATADIR%%/TemplateBatchFiles/GA_CHC.ibf %%DATADIR%%/TemplateBatchFiles/GA_CHC_Binary.ibf @@ -131,7 +134,6 @@ bin/hyphy %%DATADIR%%/TemplateBatchFiles/LocalMolClock.bf %%DATADIR%%/TemplateBatchFiles/MGvsGY.bf %%DATADIR%%/TemplateBatchFiles/MSS-joint-fitter.bf -%%DATADIR%%/TemplateBatchFiles/MSS-selector-2.bf %%DATADIR%%/TemplateBatchFiles/MSS-selector.bf %%DATADIR%%/TemplateBatchFiles/MergeSequences.bf %%DATADIR%%/TemplateBatchFiles/MergeSites.bf diff --git a/biology/kmcp/Makefile b/biology/kmcp/Makefile index 8abd37ffec4b..436e9292944d 100644 --- a/biology/kmcp/Makefile +++ b/biology/kmcp/Makefile @@ -1,7 +1,7 @@ PORTNAME= kmcp DISTVERSIONPREFIX= v DISTVERSION= 0.9.4 -PORTREVISION= 13 +PORTREVISION= 14 CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org diff --git a/biology/libgtextutils/Makefile b/biology/libgtextutils/Makefile index 2911dd8858a0..42de16d77368 100644 --- a/biology/libgtextutils/Makefile +++ b/biology/libgtextutils/Makefile @@ -8,7 +8,7 @@ WWW= https://github.com/agordon/libgtextutils LICENSE= AGPLv3 -USES= autoreconf libtool pathfix pkgconfig +USES= autoreconf libtool pkgconfig GNU_CONFIGURE= yes USE_LDCONFIG= yes diff --git a/biology/libsbml/Makefile b/biology/libsbml/Makefile index 6e771892526e..390ddab2f5f5 100644 --- a/biology/libsbml/Makefile +++ b/biology/libsbml/Makefile @@ -13,7 +13,7 @@ WWW= https://sbml.org/software/libsbml/ \ LICENSE= LGPL21 LICENSE_FILE= ${WRKSRC}/COPYING.txt -USES= cmake:testing iconv:build pathfix +USES= cmake:testing iconv:build CMAKE_OFF= EXIT_ON_ERROR \ LIBSBML_SKIP_SHARED_LIBRARY \ diff --git a/biology/linux-foldingathome/Makefile b/biology/linux-foldingathome/Makefile index b9948103d97d..7df5db1a03c8 100644 --- a/biology/linux-foldingathome/Makefile +++ b/biology/linux-foldingathome/Makefile @@ -1,9 +1,9 @@ PORTNAME= foldingathome DISTVERSION= 8.4.9 CATEGORIES= biology linux -MASTER_SITES= https://download.foldingathome.org/releases/public/fah-client/debian-10-64bit/release/ +MASTER_SITES= https://download.foldingathome.org/releases/public/fah-client/ PKGNAMEPREFIX= linux- -DISTNAME= fah-client_${DISTVERSION}-64bit-release +DISTNAME= ${_DISTNAME_${ARCH}} MAINTAINER= 0mp@FreeBSD.org COMMENT= Folding@home Client @@ -16,7 +16,7 @@ LICENSE_FILE= ${WRKSRC}/${DISTNAME}/LICENSE LICENSE_PERMS= no-dist-mirror no-dist-sell no-pkg-mirror no-pkg-sell \ auto-accept -ONLY_FOR_ARCHS= amd64 +ONLY_FOR_ARCHS= aarch64 amd64 ONLY_FOR_ARCHS_REASON= has not been ported to this architecture USES= linux:rl9 tar:bz2 @@ -46,6 +46,14 @@ _FAHCLIENT_CONFIG_XML= ${ETCDIR}/config.xml _FAHCLIENT_WORK_DIR= /var/db/fahclient _FAHCLIENT_PROGRAM= ${PREFIX}/bin/fah-client +# The base name of the distribution file is the same for all supported +# architectures, so we need to work around that in a creative way. +_DISTNAME_amd64= debian-10-64bit/release/fah-client_${DISTVERSION}-64bit-release +_DISTNAME_aarch64= debian-stable-arm64/release/fah-client_${DISTVERSION}-64bit-release +.if make(makesum) +DISTFILES= ${ONLY_FOR_ARCHS:@.ARCH.@${_DISTNAME_${.ARCH.}}${EXTRACT_SUFX}@} +.endif + do-install: ${INSTALL_PROGRAM} ${WRKSRC}/${DISTNAME}/fah-client ${STAGEDIR}${PREFIX}/bin/ @${MKDIR} ${STAGEDIR}${ETCDIR} diff --git a/biology/linux-foldingathome/distinfo b/biology/linux-foldingathome/distinfo index 39784f4f8008..8db90e6fd74a 100644 --- a/biology/linux-foldingathome/distinfo +++ b/biology/linux-foldingathome/distinfo @@ -1,3 +1,5 @@ -TIMESTAMP = 1739437601 -SHA256 (fah-client_8.4.9-64bit-release.tar.bz2) = 2acccbeda05649f6f913d29f91a22308e88ec3e117499f636a18dc56244d6cf1 -SIZE (fah-client_8.4.9-64bit-release.tar.bz2) = 3649371 +TIMESTAMP = 1755790886 +SHA256 (debian-stable-arm64/release/fah-client_8.4.9-64bit-release.tar.bz2) = 14ea352a42be0d34a1a0e2a4b46139e03d619a56bdd4908faaa56dc2665fcf3b +SIZE (debian-stable-arm64/release/fah-client_8.4.9-64bit-release.tar.bz2) = 3667080 +SHA256 (debian-10-64bit/release/fah-client_8.4.9-64bit-release.tar.bz2) = 2acccbeda05649f6f913d29f91a22308e88ec3e117499f636a18dc56244d6cf1 +SIZE (debian-10-64bit/release/fah-client_8.4.9-64bit-release.tar.bz2) = 3649371 diff --git a/biology/ncbi-blast+/Makefile b/biology/ncbi-blast+/Makefile index bf3541b88534..1627922c6d5e 100644 --- a/biology/ncbi-blast+/Makefile +++ b/biology/ncbi-blast+/Makefile @@ -1,6 +1,5 @@ PORTNAME= ncbi-blast+ -DISTVERSION= 2.16.0 -PORTREVISION= 5 +DISTVERSION= 2.17.0 CATEGORIES= biology perl5 python MASTER_SITES= https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \ https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PORTVERSION}/ @@ -16,23 +15,13 @@ LICENSE_FILE= ${WRKSRC}/scripts/projects/blast/LICENSE ONLY_FOR_ARCHS= aarch64 amd64 powerpc64 powerpc64le riscv64 ONLY_FOR_ARCHS_REASON= Requires 64-bit processor +BUILD_DEPENDS= grpc>0:devel/grpc LIB_DEPENDS= libdw.so:devel/elfutils \ - libgcrypt.so:security/libgcrypt \ - libgmp.so:math/gmp \ - libgnutls.so:security/gnutls \ - libgpg-error.so:security/libgpg-error \ - libgrpc.so:devel/grpc \ - libhogweed.so:security/nettle \ - libidn2.so:dns/libidn2 \ liblmdb.so:databases/lmdb \ liblzo2.so:archivers/lzo2 \ - libnettle.so:security/nettle \ libnghttp2.so:www/libnghttp2 \ - libp11-kit.so:security/p11-kit \ - libpcre.so:devel/pcre \ + libpcre2-8.so:devel/pcre2 \ libsqlite3.so:databases/sqlite3 \ - libtasn1.so:security/libtasn1 \ - libtspi.so:security/trousers \ libuv.so:devel/libuv \ libzstd.so:archivers/zstd RUN_DEPENDS= p5-List-MoreUtils>=0:lang/p5-List-MoreUtils \ diff --git a/biology/ncbi-blast+/distinfo b/biology/ncbi-blast+/distinfo index fb3f8ad65194..bd9b8a595168 100644 --- a/biology/ncbi-blast+/distinfo +++ b/biology/ncbi-blast+/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1733904135 -SHA256 (ncbi-blast-2.16.0+-src.tar.gz) = 17c93cf009721023e5aecf5753f9c6a255d157561638b91b3ad7276fd6950c2b -SIZE (ncbi-blast-2.16.0+-src.tar.gz) = 28307712 +TIMESTAMP = 1753183842 +SHA256 (ncbi-blast-2.17.0+-src.tar.gz) = 502057a88e9990e34e62758be21ea474cc0ad68d6a63a2e37b2372af1e5ea147 +SIZE (ncbi-blast-2.17.0+-src.tar.gz) = 29571791 diff --git a/biology/ncbi-blast+/files/patch-grpc b/biology/ncbi-blast+/files/patch-grpc deleted file mode 100644 index 22e9dc6aee66..000000000000 --- a/biology/ncbi-blast+/files/patch-grpc +++ /dev/null @@ -1,26 +0,0 @@ ---- src/serial/grpc_integration/grpc_integration.cpp.orig 2023-05-18 18:14:23 UTC -+++ src/serial/grpc_integration/grpc_integration.cpp -@@ -113,23 +113,8 @@ static CGRPCInitializer s_GRPCInitializer; - grpc::Server::GlobalCallbacks* volatile CGRPCInitializer::sm_ServerCallbacks; - static CGRPCInitializer s_GRPCInitializer; - --extern "C" { -- static void s_NCBI_GPR_Log_Function(gpr_log_func_args *args) { -- static const char* unk_func = g_DiagUnknownFunction(); -- CDiagCompileInfo diag_info(args->file, args->line, unk_func, "GRPC"); -- EDiagSev sev = eDiag_Error; -- switch (args->severity) { -- case GPR_LOG_SEVERITY_DEBUG: sev = eDiag_Trace; break; -- case GPR_LOG_SEVERITY_INFO: sev = eDiag_Info; break; -- case GPR_LOG_SEVERITY_ERROR: sev = eDiag_Error; break; -- } -- CNcbiDiag(diag_info) << Severity(sev) << args->message << Endm; -- } --} -- - CGRPCInitializer::CGRPCInitializer(void) - { -- gpr_set_log_function(s_NCBI_GPR_Log_Function); - sm_ServerCallbacks = new CGRPCServerCallbacks; - grpc::Server::SetGlobalCallbacks(sm_ServerCallbacks); - // NB: on the client side, we encourage the use of diff --git a/biology/ncbi-blast+/files/patch-src_serial_grpc__integration_grpc__integration.cpp b/biology/ncbi-blast+/files/patch-src_serial_grpc__integration_grpc__integration.cpp new file mode 100644 index 000000000000..18f4558d0310 --- /dev/null +++ b/biology/ncbi-blast+/files/patch-src_serial_grpc__integration_grpc__integration.cpp @@ -0,0 +1,32 @@ +--- src/serial/grpc_integration/grpc_integration.cpp.orig 2025-07-22 11:26:40 UTC ++++ src/serial/grpc_integration/grpc_integration.cpp +@@ -87,21 +87,6 @@ static CNCBILogSink s_NCBILogSink; + + #else //ABSEIL_LOG + +-extern "C" { +- static void s_NCBI_GPR_Log_Function(gpr_log_func_args *args) { +- static const char* unk_func = ncbi::g_DiagUnknownFunction(); +- ncbi::CDiagCompileInfo diag_info(args->file, args->line, unk_func, "GRPC"); +- ncbi::EDiagSev sev = ncbi::eDiag_Error; +- switch (args->severity) { +- case GPR_LOG_SEVERITY_DEBUG: sev = ncbi::eDiag_Trace; break; +- case GPR_LOG_SEVERITY_INFO: sev = ncbi::eDiag_Info; break; +- case GPR_LOG_SEVERITY_ERROR: sev = ncbi::eDiag_Error; break; +- } +- ncbi::CNcbiDiag(diag_info) << ncbi::Severity(sev) << args->message << ncbi::Endm; +- } +-} +-#define GPR_SET_LOG_FUNCION gpr_set_log_function(s_NCBI_GPR_Log_Function) +- + #endif //ABSEIL_LOG + #endif //HAVE_LIBGRPC + +@@ -172,7 +157,6 @@ CGRPCInitializer::CGRPCInitializer(void) + + CGRPCInitializer::CGRPCInitializer(void) + { +- GPR_SET_LOG_FUNCION; + sm_ServerCallbacks = new CGRPCServerCallbacks; + grpc::Server::SetGlobalCallbacks(sm_ServerCallbacks); + // NB: on the client side, we encourage the use of diff --git a/biology/ncbi-blast+/pkg-plist b/biology/ncbi-blast+/pkg-plist index a44c7748df28..64e087878999 100644 --- a/biology/ncbi-blast+/pkg-plist +++ b/biology/ncbi-blast+/pkg-plist @@ -14,7 +14,6 @@ bin/datatool bin/deltablast bin/dustmasker bin/gc_cli -bin/gene_info_reader bin/get_species_taxids.sh bin/legacy_blast.pl bin/lmdbxx_sample @@ -267,6 +266,7 @@ include/ncbi-tools++/cgi/cgiapp_cached.hpp include/ncbi-tools++/cgi/cgictx.hpp include/ncbi-tools++/cgi/error_codes.hpp include/ncbi-tools++/cgi/fcgiapp_mt.hpp +include/ncbi-tools++/cgi/fcgiapp_st.hpp include/ncbi-tools++/cgi/impl/cgi_entry_reader.hpp include/ncbi-tools++/cgi/ncbicgi.hpp include/ncbi-tools++/cgi/ncbicgir.hpp @@ -287,6 +287,7 @@ include/ncbi-tools++/common/ncbi_export.h include/ncbi-tools++/common/ncbi_package_ver.h include/ncbi-tools++/common/ncbi_pch_impl.hpp include/ncbi-tools++/common/ncbi_revision.h +include/ncbi-tools++/common/ncbi_sample_api.hpp include/ncbi-tools++/common/ncbi_sanitizers.h include/ncbi-tools++/common/ncbi_sc_version.h include/ncbi-tools++/common/ncbi_skew_guard.h @@ -305,6 +306,7 @@ include/ncbi-tools++/connect/ext/ncbi_dblb_svcmapper.hpp include/ncbi-tools++/connect/ext/ncbi_ifconf.h include/ncbi-tools++/connect/ext/ncbi_localnet.h include/ncbi-tools++/connect/impl/connect_misc.hpp +include/ncbi-tools++/connect/impl/ncbi_servicep.h include/ncbi-tools++/connect/impl/ncbi_uv_nghttp2.hpp include/ncbi-tools++/connect/impl/server_connection.hpp include/ncbi-tools++/connect/impl/thread_pool_for_server.hpp @@ -346,6 +348,7 @@ include/ncbi-tools++/connect/ncbi_service.h include/ncbi-tools++/connect/ncbi_service.hpp include/ncbi-tools++/connect/ncbi_service_connector.h include/ncbi-tools++/connect/ncbi_service_cxx.hpp +include/ncbi-tools++/connect/ncbi_sftp.hpp include/ncbi-tools++/connect/ncbi_socket.h include/ncbi-tools++/connect/ncbi_socket.hpp include/ncbi-tools++/connect/ncbi_socket_connector.h @@ -425,6 +428,7 @@ include/ncbi-tools++/corelib/impl/ncbi_param_impl.hpp include/ncbi-tools++/corelib/impl/ncbi_toolkit_impl.hpp include/ncbi-tools++/corelib/impl/ncbierror_impl.hpp include/ncbi-tools++/corelib/impl/rwstreambuf.hpp +include/ncbi-tools++/corelib/impl/std_backport.hpp include/ncbi-tools++/corelib/impl/stringutf8_deprecated.hpp include/ncbi-tools++/corelib/impl/stringutf8_deprecated.inl include/ncbi-tools++/corelib/interprocess_lock.hpp @@ -452,6 +456,7 @@ include/ncbi-tools++/corelib/ncbi_signal.hpp include/ncbi-tools++/corelib/ncbi_stack.hpp include/ncbi-tools++/corelib/ncbi_strings.h include/ncbi-tools++/corelib/ncbi_system.hpp +include/ncbi-tools++/corelib/ncbi_test.hpp include/ncbi-tools++/corelib/ncbi_toolkit.hpp include/ncbi-tools++/corelib/ncbi_tree.hpp include/ncbi-tools++/corelib/ncbi_url.hpp @@ -494,6 +499,7 @@ include/ncbi-tools++/corelib/ncbiutil.hpp include/ncbi-tools++/corelib/obj_pool.hpp include/ncbi-tools++/corelib/obj_store.hpp include/ncbi-tools++/corelib/perf_log.hpp +include/ncbi-tools++/corelib/phone_home_policy.hpp include/ncbi-tools++/corelib/plugin_manager.hpp include/ncbi-tools++/corelib/plugin_manager_impl.hpp include/ncbi-tools++/corelib/plugin_manager_store.hpp @@ -1901,23 +1907,6 @@ include/ncbi-tools++/objects/mim/mim__.hpp include/ncbi-tools++/objects/misc/error_codes.hpp include/ncbi-tools++/objects/misc/sequence_macros.hpp include/ncbi-tools++/objects/misc/sequence_util_macros.hpp -include/ncbi-tools++/objects/mla/.gitignore -include/ncbi-tools++/objects/mla/Error_val.hpp -include/ncbi-tools++/objects/mla/Error_val_.hpp -include/ncbi-tools++/objects/mla/Mla_back.hpp -include/ncbi-tools++/objects/mla/Mla_back_.hpp -include/ncbi-tools++/objects/mla/Mla_request.hpp -include/ncbi-tools++/objects/mla/Mla_request_.hpp -include/ncbi-tools++/objects/mla/NCBI_MedArchive_module.hpp -include/ncbi-tools++/objects/mla/Title_msg.hpp -include/ncbi-tools++/objects/mla/Title_msg_.hpp -include/ncbi-tools++/objects/mla/Title_msg_list.hpp -include/ncbi-tools++/objects/mla/Title_msg_list_.hpp -include/ncbi-tools++/objects/mla/Title_type.hpp -include/ncbi-tools++/objects/mla/Title_type_.hpp -include/ncbi-tools++/objects/mla/mla__.hpp -include/ncbi-tools++/objects/mla/mla_client.hpp -include/ncbi-tools++/objects/mla/mla_client_.hpp include/ncbi-tools++/objects/mmdb1/.gitignore include/ncbi-tools++/objects/mmdb1/Atom.hpp include/ncbi-tools++/objects/mmdb1/Atom_.hpp @@ -3339,6 +3328,7 @@ include/ncbi-tools++/objmgr/impl/bioseq_edit_commands.hpp include/ncbi-tools++/objmgr/impl/bioseq_info.hpp include/ncbi-tools++/objmgr/impl/bioseq_set_edit_commands.hpp include/ncbi-tools++/objmgr/impl/bioseq_set_info.hpp +include/ncbi-tools++/objmgr/impl/bioseq_sort.hpp include/ncbi-tools++/objmgr/impl/data_source.hpp include/ncbi-tools++/objmgr/impl/edit_commands_impl.hpp include/ncbi-tools++/objmgr/impl/handle_range.hpp @@ -3483,11 +3473,7 @@ include/ncbi-tools++/objtools/blast/blastdb_format/blastdb_seqid.hpp include/ncbi-tools++/objtools/blast/blastdb_format/invalid_data_exception.hpp include/ncbi-tools++/objtools/blast/blastdb_format/seq_formatter.hpp include/ncbi-tools++/objtools/blast/blastdb_format/seq_writer.hpp -include/ncbi-tools++/objtools/blast/gene_info_reader/file_utils.hpp -include/ncbi-tools++/objtools/blast/gene_info_reader/gene_info.hpp -include/ncbi-tools++/objtools/blast/gene_info_reader/gene_info_reader.hpp include/ncbi-tools++/objtools/blast/seqdb_reader/column_reader.hpp -include/ncbi-tools++/objtools/blast/seqdb_reader/impl/lmdb++.h include/ncbi-tools++/objtools/blast/seqdb_reader/impl/seqdb_lmdb.hpp include/ncbi-tools++/objtools/blast/seqdb_reader/impl/seqdbatlas.hpp include/ncbi-tools++/objtools/blast/seqdb_reader/impl/seqdbcol.hpp @@ -3551,7 +3537,13 @@ include/ncbi-tools++/objtools/data_loaders/genbank/impl/incr_time.hpp include/ncbi-tools++/objtools/data_loaders/genbank/impl/info_cache.hpp include/ncbi-tools++/objtools/data_loaders/genbank/impl/processor.hpp include/ncbi-tools++/objtools/data_loaders/genbank/impl/processors.hpp +include/ncbi-tools++/objtools/data_loaders/genbank/impl/psg_blob_processor.hpp +include/ncbi-tools++/objtools/data_loaders/genbank/impl/psg_cache.hpp +include/ncbi-tools++/objtools/data_loaders/genbank/impl/psg_cdd.hpp +include/ncbi-tools++/objtools/data_loaders/genbank/impl/psg_evloop.hpp include/ncbi-tools++/objtools/data_loaders/genbank/impl/psg_loader_impl.hpp +include/ncbi-tools++/objtools/data_loaders/genbank/impl/psg_processor.hpp +include/ncbi-tools++/objtools/data_loaders/genbank/impl/psg_processors.hpp include/ncbi-tools++/objtools/data_loaders/genbank/impl/reader_id1_base.hpp include/ncbi-tools++/objtools/data_loaders/genbank/impl/reader_id2_base.hpp include/ncbi-tools++/objtools/data_loaders/genbank/impl/reader_service.hpp @@ -4513,6 +4505,7 @@ include/ncbi-tools++/objtools/readers/aln_reader.hpp include/ncbi-tools++/objtools/readers/alnread.hpp include/ncbi-tools++/objtools/readers/bed_reader.hpp include/ncbi-tools++/objtools/readers/cigar.hpp +include/ncbi-tools++/objtools/readers/co_generator.hpp include/ncbi-tools++/objtools/readers/error_container.hpp include/ncbi-tools++/objtools/readers/fasta.hpp include/ncbi-tools++/objtools/readers/fasta_exception.hpp @@ -4687,6 +4680,7 @@ include/ncbi-tools++/sra/readers/bam/bgzf.hpp include/ncbi-tools++/sra/readers/bam/cache_with_lock.hpp include/ncbi-tools++/sra/readers/bam/vdbfile.hpp include/ncbi-tools++/sra/readers/ncbi_traces_path.hpp +include/ncbi-tools++/sra/readers/ncbi_traces_path.hpp.bak include/ncbi-tools++/sra/readers/sra/csraread.hpp include/ncbi-tools++/sra/readers/sra/exception.hpp include/ncbi-tools++/sra/readers/sra/graphread.hpp @@ -4784,6 +4778,10 @@ include/ncbi-tools++/util/compress/zlib.hpp include/ncbi-tools++/util/compress/zlib/zconf.h include/ncbi-tools++/util/compress/zlib/zlib.h include/ncbi-tools++/util/compress/zlib/zutil.h +include/ncbi-tools++/util/compress/zlib_cloudflare.hpp +include/ncbi-tools++/util/compress/zlib_cloudflare/zconf_cf.h +include/ncbi-tools++/util/compress/zlib_cloudflare/zlib_cf.h +include/ncbi-tools++/util/compress/zlib_cloudflare/zutil_cf.h include/ncbi-tools++/util/compress/zstd.hpp include/ncbi-tools++/util/creaders/alnread.h include/ncbi-tools++/util/creaders/creaders_export.h @@ -4801,15 +4799,13 @@ include/ncbi-tools++/util/histogram_binning.hpp include/ncbi-tools++/util/icanceled.hpp include/ncbi-tools++/util/id_mux.hpp include/ncbi-tools++/util/impl/compile_time_bits.hpp -include/ncbi-tools++/util/impl/const_tuple.hpp -include/ncbi-tools++/util/impl/ct_bitset_cxx14.hpp include/ncbi-tools++/util/impl/ct_bitset_cxx17.hpp include/ncbi-tools++/util/impl/ct_crc32.hpp -include/ncbi-tools++/util/impl/ct_string_cxx14.hpp include/ncbi-tools++/util/impl/ct_string_cxx17.hpp include/ncbi-tools++/util/impl/ctsort_cxx14.hpp include/ncbi-tools++/util/impl/floating_point_comparison.hpp include/ncbi-tools++/util/impl/generated_fsm.hpp +include/ncbi-tools++/util/incr_time.hpp include/ncbi-tools++/util/itransaction.hpp include/ncbi-tools++/util/itree.hpp include/ncbi-tools++/util/itree.inl @@ -4826,6 +4822,7 @@ include/ncbi-tools++/util/math/matrix.hpp include/ncbi-tools++/util/math/miscmath.h include/ncbi-tools++/util/math/promote.hpp include/ncbi-tools++/util/md5.hpp +include/ncbi-tools++/util/memory_streambuf.hpp include/ncbi-tools++/util/message_queue.hpp include/ncbi-tools++/util/miscmath.h include/ncbi-tools++/util/multi_writer.hpp @@ -4847,10 +4844,8 @@ include/ncbi-tools++/util/regexp.hpp include/ncbi-tools++/util/regexp/ctre/LICENSE include/ncbi-tools++/util/regexp/ctre/ctre-unicode.hpp include/ncbi-tools++/util/regexp/ctre/ctre.hpp -include/ncbi-tools++/util/regexp/pcre.h -include/ncbi-tools++/util/regexp/pcrecpp.h -include/ncbi-tools++/util/regexp/pcrecpparg.h -include/ncbi-tools++/util/regexp/pcreposix.h +include/ncbi-tools++/util/regexp/pcre2.h +include/ncbi-tools++/util/regexp/pcre2posix.h include/ncbi-tools++/util/request_control.hpp include/ncbi-tools++/util/resize_iter.hpp include/ncbi-tools++/util/resource_pool.hpp @@ -4984,8 +4979,6 @@ lib/ncbi-tools++/libgbseq-static.a lib/ncbi-tools++/libgbseq.a lib/ncbi-tools++/libgencoll_client-static.a lib/ncbi-tools++/libgencoll_client.a -lib/ncbi-tools++/libgene_info-static.a -lib/ncbi-tools++/libgene_info.a lib/ncbi-tools++/libgeneral-static.a lib/ncbi-tools++/libgeneral.a lib/ncbi-tools++/libgenesbyloc-static.a @@ -5020,10 +5013,6 @@ lib/ncbi-tools++/libmedline-static.a lib/ncbi-tools++/libmedline.a lib/ncbi-tools++/libmim-static.a lib/ncbi-tools++/libmim.a -lib/ncbi-tools++/libmla-static.a -lib/ncbi-tools++/libmla.a -lib/ncbi-tools++/libmlacli-static.a -lib/ncbi-tools++/libmlacli.a lib/ncbi-tools++/libmmdb-static.a lib/ncbi-tools++/libmmdb.a lib/ncbi-tools++/libncbi_xblobstorage_netcache-static.a @@ -5206,3 +5195,5 @@ lib/ncbi-tools++/libxxconnect.a lib/ncbi-tools++/libxxconnect2-dll.so lib/ncbi-tools++/libxxconnect2-static.a lib/ncbi-tools++/libxxconnect2.a +lib/ncbi-tools++/libzcf-static.a +lib/ncbi-tools++/libzcf.a diff --git a/biology/ncbi-entrez-direct/Makefile b/biology/ncbi-entrez-direct/Makefile index 4b1aae4c4156..85ba1fe80dd4 100644 --- a/biology/ncbi-entrez-direct/Makefile +++ b/biology/ncbi-entrez-direct/Makefile @@ -1,6 +1,6 @@ PORTNAME= ncbi-entrez-direct DISTVERSION= 14.9.20210423 -PORTREVISION= 29 +PORTREVISION= 30 CATEGORIES= biology perl5 MASTER_SITES= ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/${PORTVERSION}/ DISTFILES= edirect.tar.gz diff --git a/biology/plink/Makefile b/biology/plink/Makefile index fd08152bc388..ca5cd584fc19 100644 --- a/biology/plink/Makefile +++ b/biology/plink/Makefile @@ -11,7 +11,7 @@ WWW= https://www.cog-genomics.org/plink/ LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE -NOT_FOR_ARCHS= aarch64 mips64 powerpc64 powerpc64le +NOT_FOR_ARCHS= aarch64 mips64 powerpc64 NOT_FOR_ARCHS_REASON= 64bit code requires SSE2 instructions USES= gmake fortran @@ -25,6 +25,7 @@ WRKSRC_SUBDIR= 1.9 MAKEFILE= Makefile.std MAKE_ARGS= ZLIB=-lz BLASFLAGS="${BLASLIB} ${LAPACKLIB}" CFLAGS+= -DDYNAMIC_ZLIB -I${LOCALBASE}/include +CFLAGS_powerpc64le= -DNO_WARN_X86_INTRINSICS -D__SSE2__ LDFLAGS+= -lthr INSTALL_TARGET= install-strip diff --git a/biology/py-bx-python/Makefile b/biology/py-bx-python/Makefile index 6b66a17d1250..309fa98df6ca 100644 --- a/biology/py-bx-python/Makefile +++ b/biology/py-bx-python/Makefile @@ -1,6 +1,5 @@ PORTNAME= bx-python -DISTVERSION= 0.13.0 -PORTREVISION= 1 +DISTVERSION= 0.14.0 CATEGORIES= biology python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -14,11 +13,18 @@ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYNUMPY} -BUILD_DEPENDS= ${PY_DEPENDS} -RUN_DEPENDS= ${PY_DEPENDS} +BUILD_DEPENDS= ${PY_SETUPTOOLS} \ + ${PY_DEPENDS} \ + ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} +RUN_DEPENDS= ${PY_DEPENDS} \ + ${PYTHON_PKGNAMEPREFIX}pyparsing>0:devel/py-pyparsing@${PY_FLAVOR} USES= compiler python -USE_PYTHON= autoplist cython3 distutils +USE_PYTHON= pep517 cython3 autoplist + +post-patch: + # force cythonization, compilation fails otherwise for some reason + @${TOUCH} `${FIND} ${WRKSRC} -name "*.pyx" -o -name "*.pxd"` post-install: @${FIND} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/bx -name "*.so" | ${XARGS} ${STRIP_CMD} diff --git a/biology/py-bx-python/distinfo b/biology/py-bx-python/distinfo index 56d00203a687..85e09edf789a 100644 --- a/biology/py-bx-python/distinfo +++ b/biology/py-bx-python/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1734273029 -SHA256 (bx_python-0.13.0.tar.gz) = ce04696543367efc6b7995d9463efeda691b9a58f6f55a7bd831e642159b0644 -SIZE (bx_python-0.13.0.tar.gz) = 1899129 +TIMESTAMP = 1756062999 +SHA256 (bx_python-0.14.0.tar.gz) = c46eef1006d6107e31d2ff42f1ca27c34ddb080151309a909b4d2e53ca812cc6 +SIZE (bx_python-0.14.0.tar.gz) = 2085934 diff --git a/biology/py-htseq/Makefile b/biology/py-htseq/Makefile index 45519bfbd69f..68a608f3c79c 100644 --- a/biology/py-htseq/Makefile +++ b/biology/py-htseq/Makefile @@ -6,7 +6,7 @@ MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} DISTNAME= ${PORTNAME:tl}-${DISTVERSION} -MAINTAINER= alster@vinterdalen.se +MAINTAINER= alven@FreeBSD.org COMMENT= Python library to facilitate programmatic analysis of sequence data WWW= https://github.com/htseq/htseq/ diff --git a/biology/salmon/Makefile b/biology/salmon/Makefile index 74631d470a17..8332ba416d74 100644 --- a/biology/salmon/Makefile +++ b/biology/salmon/Makefile @@ -1,7 +1,6 @@ PORTNAME= salmon DISTVERSIONPREFIX= v -DISTVERSION= 1.10.2 -PORTREVISION= 8 +DISTVERSION= 1.10.3 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -20,18 +19,23 @@ BUILD_DEPENDS= bash:shells/bash \ libgff==2.0.0:biology/libgff \ libtool:devel/libtool \ autoreconf:devel/autoconf \ - aclocal:devel/automake -LIB_DEPENDS= libboost_system.so:devel/boost-libs \ - libtbb.so:devel/onetbb \ - libcurl.so:ftp/curl + aclocal:devel/automake \ + eigen>0:math/eigen3 \ + libdivide>0:math/libdivide \ + curl>0:ftp/curl +LIB_DEPENDS= libtbb.so:devel/onetbb USES= cmake:noninja gmake localbase shebangfix USE_GITHUB= yes +# Can't unbundle io_lib unless we also unbundle htscodecs from io_lib, +# which is a nightmare: explicitly integrated into configure files and +# installs htscodecs files, conflicting with separate htscodecs port. GH_ACCOUNT= COMBINE-lab -GH_TUPLE+= COMBINE-lab:pufferfish:salmon-v1.10.2:pf/external/pufferfish -GH_TUPLE+= jkbonfield:io_lib:io_lib-1-14-15:sio/external/staden-io_lib -GH_TUPLE+= samtools:htscodecs:5aecc6e:htscodec/external/staden-io_lib/htscodecs +GH_TUPLE+= COMBINE-lab:pufferfish:salmon-v${DISTVERSION}:pf/external/pufferfish +GH_TUPLE+= jkbonfield:io_lib:io_lib-1-15-1:sio/external/staden-io_lib +# Update commit hash from io_lib release branch +GH_TUPLE+= samtools:htscodecs:de42211:htscodec/external/staden-io_lib/htscodecs SHEBANG_FILES= scripts/* PLIST_FILES= bin/salmon @@ -40,9 +44,13 @@ CMAKE_ARGS+= -DHAVE_FAST_MALLOC:BOOL=on \ -DFETCHED_PUFFERFISH:BOOL=on \ -DFETCHED_LIBGFF:BOOL=on \ -DFETCH_STADEN:BOOL=true +WITH_DEBUG= yes +CXXFLAGS+= -I${LOCALBASE}/include/eigen3 LDFLAGS+= -lpthread pre-configure: + ${RM} -rf ${WRKSRC}/include/eigen3 \ + ${WRKSRC}/external/pufferfish/include/libdivide (cd ${WRKSRC}/external/staden-io_lib && ./bootstrap) do-install: diff --git a/biology/salmon/distinfo b/biology/salmon/distinfo index 42eb0d9ee404..ea5ed9dddde3 100644 --- a/biology/salmon/distinfo +++ b/biology/salmon/distinfo @@ -1,9 +1,9 @@ -TIMESTAMP = 1689958260 -SHA256 (COMBINE-lab-salmon-v1.10.2_GH0.tar.gz) = 976989182160fef3afb4429ee8b85d8dd39ed6ca212bb14d6a65cde0e985fb98 -SIZE (COMBINE-lab-salmon-v1.10.2_GH0.tar.gz) = 7193261 -SHA256 (COMBINE-lab-pufferfish-salmon-v1.10.2_GH0.tar.gz) = b90ce8079c375136d12e37bc23e451ae34a49d49c54f6cdd2050ba8add758ab4 -SIZE (COMBINE-lab-pufferfish-salmon-v1.10.2_GH0.tar.gz) = 3368053 -SHA256 (jkbonfield-io_lib-io_lib-1-14-15_GH0.tar.gz) = 4444c78846e49a493ff09d56d55ebe61140bb0a76ec5fa1c27eff13ec9dabd8b -SIZE (jkbonfield-io_lib-io_lib-1-14-15_GH0.tar.gz) = 3382074 -SHA256 (samtools-htscodecs-5aecc6e_GH0.tar.gz) = 3abb6a8516761bf0db5149c3d6c077e2d540470180245c2afb1f4400158b1f54 -SIZE (samtools-htscodecs-5aecc6e_GH0.tar.gz) = 3191442 +TIMESTAMP = 1753565795 +SHA256 (COMBINE-lab-salmon-v1.10.3_GH0.tar.gz) = a053fba63598efc4ade3684aa2c8e8e2294186927d4fcdf1041c36edc2aa0871 +SIZE (COMBINE-lab-salmon-v1.10.3_GH0.tar.gz) = 7193092 +SHA256 (COMBINE-lab-pufferfish-salmon-v1.10.3_GH0.tar.gz) = 5d345ba30f22ff4448f4bf2920d2246a11cc38b203e12828c07b2612e41d2951 +SIZE (COMBINE-lab-pufferfish-salmon-v1.10.3_GH0.tar.gz) = 3368105 +SHA256 (jkbonfield-io_lib-io_lib-1-15-1_GH0.tar.gz) = 5fef32bb10991b388b4a92292e58d6ef8e7eda812ab2d6a10daaca9a757e6302 +SIZE (jkbonfield-io_lib-io_lib-1-15-1_GH0.tar.gz) = 3381908 +SHA256 (samtools-htscodecs-de42211_GH0.tar.gz) = 65e632bf00e2e456a3040e8a4748dbd33161595029ba49dec89d5301ebdd4de6 +SIZE (samtools-htscodecs-de42211_GH0.tar.gz) = 3200933 diff --git a/biology/salmon/files/patch-CMakeLists.txt b/biology/salmon/files/patch-CMakeLists.txt index 5a6bd2de2f02..36038f452843 100644 --- a/biology/salmon/files/patch-CMakeLists.txt +++ b/biology/salmon/files/patch-CMakeLists.txt @@ -1,11 +1,11 @@ ---- CMakeLists.txt.orig 2023-07-21 14:03:31 UTC +--- CMakeLists.txt.orig 2025-07-26 11:52:41 UTC +++ CMakeLists.txt @@ -310,14 +310,16 @@ endif() # Grab pufferfish source --- DURING CONFIGURE TIME! # #### -if(NOT FETCHED_PUFFERFISH) -+ ++# if(NOT FETCHED_PUFFERFISH) +# Fetched by GH_TUPLE in FreeBSD port +# if(NOT FETCHED_PUFFERFISH) exec_program(${CMAKE_CURRENT_SOURCE_DIR}/scripts/fetchPufferfish.sh RETURN_VALUE FETCH_PF_SCRIPT_RET) @@ -19,11 +19,12 @@ ## # Super-secret override -@@ -364,7 +366,10 @@ if(NOT Iconv_IS_BUILT_IN) +@@ -364,7 +366,11 @@ endif() set(ICONV_LIB Iconv::Iconv) endif() -find_package(LibLZMA) ++# find_package(LibLZMA) +# lzma is in FreeBSD base +# find_package(LibLZMA) +set(LIBLZMA_FOUND TRUE) @@ -31,29 +32,35 @@ if(NOT LIBLZMA_FOUND) message("Will attempt to fetch and build liblzma") message("=======================================") -@@ -381,8 +386,8 @@ externalproject_add(liblzma +@@ -381,8 +387,11 @@ externalproject_add(liblzma INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install BUILD_IN_SOURCE TRUE CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.2/configure --prefix=<INSTALL_DIR> CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CFLAGS=${EXTRA_CMAKE_INCLUDE_FLAGS} CPPFLAGS=${EXTRA_CMAKE_INCLUDE_FLAGS} LDFLAGS=${EXTRA_CMAKE_LIBRARY_FLAGS} - BUILD_COMMAND make ${QUIET_MAKE} - INSTALL_COMMAND make ${QUIET_MAKE} install ++# BUILD_COMMAND make ${QUIET_MAKE} ++# INSTALL_COMMAND make ${QUIET_MAKE} install ++# FreeBSD make is bsdmake + BUILD_COMMAND gmake ${QUIET_MAKE} + INSTALL_COMMAND gmake ${QUIET_MAKE} install ) # Tell cmake that the external project generated a library so we can -@@ -411,8 +416,8 @@ externalproject_add(libbz2 +@@ -411,8 +420,11 @@ externalproject_add(libbz2 INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install BUILD_IN_SOURCE TRUE CONFIGURE_COMMAND "" - BUILD_COMMAND make ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} - INSTALL_COMMAND make ${QUIET_MAKE} install PREFIX=<INSTALL_DIR> ++# BUILD_COMMAND make ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ++# INSTALL_COMMAND make ${QUIET_MAKE} install PREFIX=<INSTALL_DIR> ++# FreeBSD make is bsdmake + BUILD_COMMAND gmake ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} + INSTALL_COMMAND gmake ${QUIET_MAKE} install PREFIX=<INSTALL_DIR> ) # Tell cmake that the external project generated a library so we can # add dependencies here instead of later -@@ -609,9 +614,11 @@ if (NOT CEREAL_FOUND) +@@ -577,9 +589,11 @@ endif() endif() ## Try and find TBB first @@ -68,53 +75,78 @@ if (${TBB_FOUND}) if (${TBB_VERSION} VERSION_GREATER_EQUAL 2021.4) -@@ -791,22 +798,16 @@ endif() +@@ -761,25 +775,28 @@ if (NOT LIBSTADENIO_FOUND) if (NOT LIBSTADENIO_FOUND) message("Build system will compile Staden IOLib") message("==================================================================") + # stadenio is downloaded by GH_TUPLE in FreeBSD port externalproject_add(libstadenio - DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -- DOWNLOAD_COMMAND curl -k -L https://github.com/jkbonfield/io_lib/releases/download/io_lib-1-14-15/io_lib-1.14.15.tar.gz -o staden-io_lib-v1.14.15.tar.gz && -- ${SHASUM} 20814c4365e1e2fe6630fb11d0df370dec4c5688af3871de7f1cb0129671401e staden-io_lib-v1.14.15.tar.gz && -- mkdir -p staden-io_lib-1.14.15 && -- tar -xzf staden-io_lib-v1.14.15.tar.gz --strip-components=1 -C staden-io_lib-1.14.15 && +- DOWNLOAD_COMMAND curl -k -L https://github.com/jkbonfield/io_lib/releases/download/io_lib-1-15-0/io_lib-1.15.0.tar.gz -o staden-io_lib-v1.15.0.tar.gz && +- ${SHASUM} ad343dac7c77086db1b54585c5887b26eda6430d1639d111dd3304c3b749494f staden-io_lib-v1.15.0.tar.gz && +- mkdir -p staden-io_lib-1.15.0 && +- tar -xzf staden-io_lib-v1.15.0.tar.gz --strip-components=1 -C staden-io_lib-1.15.0 && - rm -fr staden-io_lib && -- mv -f staden-io_lib-1.14.15 staden-io_lib +- mv -f staden-io_lib-1.15.0 staden-io_lib && +- curl -k -L https://github.com/samtools/htscodecs/releases/download/v1.6.0/htscodecs-1.6.0.tar.gz -o htscodecs-1.6.0.tar.gz && +- mkdir -p htscodecs-1.6.0 && +- tar -xzf htscodecs-1.6.0.tar.gz --strip-components=1 -C htscodecs-1.6.0 && +- rm -fr staden-io_lib/htscodecs && +- mv -f htscodecs-1.6.0 staden-io_lib/htscodecs ++ # DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external ++ # DOWNLOAD_COMMAND curl -k -L https://github.com/jkbonfield/io_lib/releases/download/io_lib-1-15-0/io_lib-1.15.0.tar.gz -o staden-io_lib-v1.15.0.tar.gz && ++ # ${SHASUM} ad343dac7c77086db1b54585c5887b26eda6430d1639d111dd3304c3b749494f staden-io_lib-v1.15.0.tar.gz && ++ # mkdir -p staden-io_lib-1.15.0 && ++ # tar -xzf staden-io_lib-v1.15.0.tar.gz --strip-components=1 -C staden-io_lib-1.15.0 && ++ # rm -fr staden-io_lib && ++ # mv -f staden-io_lib-1.15.0 staden-io_lib && ++ # curl -k -L https://github.com/samtools/htscodecs/releases/download/v1.6.0/htscodecs-1.6.0.tar.gz -o htscodecs-1.6.0.tar.gz && ++ # mkdir -p htscodecs-1.6.0 && ++ # tar -xzf htscodecs-1.6.0.tar.gz --strip-components=1 -C htscodecs-1.6.0 && ++ # rm -fr staden-io_lib/htscodecs && ++ # mv -f htscodecs-1.6.0 staden-io_lib/htscodecs SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/staden-io_lib INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install CONFIGURE_COMMAND ./configure --enable-shared=no --without-libcurl --prefix=<INSTALL_DIR> LDFLAGS=${LIBSTADEN_LDFLAGS} CFLAGS=${LIBSTADEN_CFLAGS} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} - BUILD_COMMAND make ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CFLAGS+=${STADEN_INC} CFLAGS+=${STADEN_LIB} LDFLAGS+=${EXTRA_CMAKE_LIBRARY_FLAGS} CFLAGS+=${EXTRA_CMAKE_INCLUDE_FLAGS} CFLAGS+=${LZFLAG} CFLAGS+=${SCHAR_FLAG} ++ # FreeBSD make is bsdmake + BUILD_COMMAND gmake ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CFLAGS+=${STADEN_INC} CFLAGS+=${STADEN_LIB} LDFLAGS+=${EXTRA_CMAKE_LIBRARY_FLAGS} CFLAGS+=${EXTRA_CMAKE_INCLUDE_FLAGS} CFLAGS+=${LZFLAG} CFLAGS+=${SCHAR_FLAG} - - BUILD_IN_SOURCE 1 - INSTALL_COMMAND make install ++ # FreeBSD make is bsdmake + INSTALL_COMMAND gmake install ) if(NOT LIBLZMA_FOUND) ExternalProject_Add_StepDependencies(libstadenio build liblzma) -@@ -820,23 +821,9 @@ if (ASAN_BUILD) +@@ -793,23 +810,26 @@ else() set(FAST_MALLOC_LIB "") set(HAVE_FAST_MALLOC TRUE) else() - set(FAST_MALLOC_LIB "") - set(HAVE_FAST_MALLOC FALSE) -- -- # See if we have Jemalloc ++ # set(FAST_MALLOC_LIB "") ++ # set(HAVE_FAST_MALLOC FALSE) + + # See if we have Jemalloc - find_package(Jemalloc) - if(Jemalloc_FOUND) -- ## -- # Don't be so stringent about the version yet -- ## -- #if (NOT (${JEMALLOC_VERSION} VERSION_LESS 5.2.1)) ++ # find_package(Jemalloc) ++ # if(Jemalloc_FOUND) + ## + # Don't be so stringent about the version yet + ## + #if (NOT (${JEMALLOC_VERSION} VERSION_LESS 5.2.1)) - message("Found Jemalloc library --- using this memory allocator") - set(FAST_MALLOC_LIB ${JEMALLOC_LIBRARIES}) - set(HAVE_FAST_MALLOC TRUE) -- #else() -- # message("Fond Jemalloc version ${JEMALLOC_VERSION}, but require >= 5.2.1. Downloading newer version") -- #endif() ++ # message("Found Jemalloc library --- using this memory allocator") ++ # set(FAST_MALLOC_LIB ${JEMALLOC_LIBRARIES}) ++ # set(HAVE_FAST_MALLOC TRUE) + #else() + # message("Fond Jemalloc version ${JEMALLOC_VERSION}, but require >= 5.2.1. Downloading newer version") + #endif() - endif() ++ # endif() + # jemalloc is default on FreeBSD + set(FAST_MALLOC_LIB "/usr/lib/libc.so") + set(HAVE_FAST_MALLOC TRUE) diff --git a/biology/salmon/files/patch-external_pufferfish_external_twopaco_graphconstructor_candidateoccurence.h b/biology/salmon/files/patch-external_pufferfish_external_twopaco_graphconstructor_candidateoccurence.h new file mode 100644 index 000000000000..8686f1695177 --- /dev/null +++ b/biology/salmon/files/patch-external_pufferfish_external_twopaco_graphconstructor_candidateoccurence.h @@ -0,0 +1,11 @@ +--- external/pufferfish/external/twopaco/graphconstructor/candidateoccurence.h.orig 2025-07-26 13:01:27 UTC ++++ external/pufferfish/external/twopaco/graphconstructor/candidateoccurence.h +@@ -58,7 +58,7 @@ namespace TwoPaCo + const CandidateOccurence & operator = (const CandidateOccurence & toCopy) + { + body_ = toCopy.body_; +- count_ = toCopy.count_; ++ count_.store(toCopy.count_.load(std::memory_order_relaxed)); + } + + void Inc() diff --git a/biology/salmon/files/patch-external_pufferfish_src_PuffAligner.cpp b/biology/salmon/files/patch-external_pufferfish_src_PuffAligner.cpp new file mode 100644 index 000000000000..682951604abe --- /dev/null +++ b/biology/salmon/files/patch-external_pufferfish_src_PuffAligner.cpp @@ -0,0 +1,14 @@ +--- external/pufferfish/src/PuffAligner.cpp.orig 2023-06-26 19:34:50 UTC ++++ external/pufferfish/src/PuffAligner.cpp +@@ -1,7 +1,10 @@ + #include "nonstd/string_view.hpp" + #include "PuffAligner.hpp" + #include "Util.hpp" +-#include "libdivide/libdivide.h" ++// Bundled libdivide causes build failures with clang19 ++// Use FreeBSD libdivde port instead ++// #include "libdivide/libdivide.h" ++#include <libdivide.h> + + std::string extractReadSeq(const std::string& readSeq, uint32_t rstart, uint32_t rend, bool isFw) { + std::string subseq = readSeq.substr(rstart, rend - rstart); diff --git a/biology/salmon/files/patch-scripts_fetchPufferfish.sh b/biology/salmon/files/patch-scripts_fetchPufferfish.sh index 566493a5e7ee..a1885fd1ff61 100644 --- a/biology/salmon/files/patch-scripts_fetchPufferfish.sh +++ b/biology/salmon/files/patch-scripts_fetchPufferfish.sh @@ -1,15 +1,13 @@ ---- scripts/fetchPufferfish.sh.orig 2023-07-21 13:59:29 UTC +--- scripts/fetchPufferfish.sh.orig 2025-07-26 17:38:39 UTC +++ scripts/fetchPufferfish.sh -@@ -11,52 +11,12 @@ CURR_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && p +@@ -11,53 +11,6 @@ INSTALL_DIR=${CURR_DIR}/../external/install EXTERNAL_DIR=${CURR_DIR}/../external INSTALL_DIR=${CURR_DIR}/../external/install -if [ -d ${EXTERNAL_DIR}/pufferfish ] ; then - rm -fr ${EXTERNAL_DIR}/pufferfish -fi -+# Pufferfish is downloaded using GH_TUPLE in the FreeBSD port, so remove -+# code here that downloads and unpacks - +- -if [ -d ${INSTALL_DIR}/include/pufferfish ] ; then - rm -fr ${INSTALL_DIR}/include/pufferfish -fi @@ -18,11 +16,11 @@ - rm -fr ${INSTALL_DIR}/src/pufferfish -fi - - SVER=salmon-v1.10.2 - #SVER=develop - #SVER=sketch-mode +-SVER=salmon-v1.10.3 +-#SVER=develop +-#SVER=sketch-mode - --EXPECTED_SHA256=f225b74833f71dcf767a565345224357fb091f90ce79717abc836814d9ccd101 +-EXPECTED_SHA256=52b6699de0d33814b73edb3455175568c2330d8014be017dce7b564e54134860 - -mkdir -p ${EXTERNAL_DIR} -curl -k -L https://github.com/COMBINE-lab/pufferfish/archive/${SVER}.zip -o ${EXTERNAL_DIR}/pufferfish.zip @@ -52,6 +50,15 @@ -rm -fr ${EXTERNAL_DIR}/pufferfish -unzip ${EXTERNAL_DIR}/pufferfish.zip -d ${EXTERNAL_DIR} -mv ${EXTERNAL_DIR}/pufferfish-${SVER} ${EXTERNAL_DIR}/pufferfish - +- mkdir -p ${INSTALL_DIR}/include/pufferfish + cp ${EXTERNAL_DIR}/pufferfish/include/ProgOpts.hpp ${INSTALL_DIR}/include/pufferfish +@@ -90,7 +43,6 @@ cp ${EXTERNAL_DIR}/pufferfish/include/BinWriter.hpp ${ + cp ${EXTERNAL_DIR}/pufferfish/include/BulkChunk.hpp ${INSTALL_DIR}/include/pufferfish + cp ${EXTERNAL_DIR}/pufferfish/include/BinWriter.hpp ${INSTALL_DIR}/include/pufferfish + +-cp -r ${EXTERNAL_DIR}/pufferfish/include/libdivide ${INSTALL_DIR}/include/pufferfish + cp -r ${EXTERNAL_DIR}/pufferfish/include/ksw2pp ${INSTALL_DIR}/include/pufferfish + # this is now automatically tracked and inherited via twopaco (on which libpuffer depends) + # cp -r ${EXTERNAL_DIR}/pufferfish/include/compact_vector ${INSTALL_DIR}/include/pufferfish diff --git a/biology/seqkit/Makefile b/biology/seqkit/Makefile index 566dadbebf89..32feed338333 100644 --- a/biology/seqkit/Makefile +++ b/biology/seqkit/Makefile @@ -1,7 +1,7 @@ PORTNAME= seqkit DISTVERSIONPREFIX= v DISTVERSION= 2.10.0 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org diff --git a/biology/taxonkit/Makefile b/biology/taxonkit/Makefile index 55121e4f0183..af4e7ff36251 100644 --- a/biology/taxonkit/Makefile +++ b/biology/taxonkit/Makefile @@ -1,7 +1,7 @@ PORTNAME= taxonkit DISTVERSIONPREFIX= v DISTVERSION= 0.19.0 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org diff --git a/biology/unikmer/Makefile b/biology/unikmer/Makefile index 708870803ed1..96350b97b14b 100644 --- a/biology/unikmer/Makefile +++ b/biology/unikmer/Makefile @@ -1,7 +1,7 @@ PORTNAME= unikmer DISTVERSIONPREFIX= v DISTVERSION= 0.20.0 -PORTREVISION= 8 +PORTREVISION= 9 CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org |