diff options
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/augustus/Makefile | 2 | ||||
| -rw-r--r-- | biology/bbmap/Makefile | 6 | ||||
| -rw-r--r-- | biology/bbmap/distinfo | 6 | ||||
| -rw-r--r-- | biology/bbmap/pkg-plist | 412 | ||||
| -rw-r--r-- | biology/bcf-score/Makefile | 2 | ||||
| -rw-r--r-- | biology/biococoa/Makefile | 2 | ||||
| -rw-r--r-- | biology/biosig/Makefile | 2 | ||||
| -rw-r--r-- | biology/bwa/Makefile | 2 | ||||
| -rw-r--r-- | biology/kmcp/Makefile | 2 | ||||
| -rw-r--r-- | biology/ncbi-entrez-direct/Makefile | 2 | ||||
| -rw-r--r-- | biology/plink/Makefile | 3 | ||||
| -rw-r--r-- | biology/py-htseq/Makefile | 2 | ||||
| -rw-r--r-- | biology/salmon/Makefile | 26 | ||||
| -rw-r--r-- | biology/salmon/distinfo | 18 | ||||
| -rw-r--r-- | biology/salmon/files/patch-CMakeLists.txt | 80 | ||||
| -rw-r--r-- | biology/salmon/files/patch-external_pufferfish_external_twopaco_graphconstructor_candidateoccurence.h | 11 | ||||
| -rw-r--r-- | biology/salmon/files/patch-external_pufferfish_src_PuffAligner.cpp | 14 | ||||
| -rw-r--r-- | biology/salmon/files/patch-scripts_fetchPufferfish.sh | 27 | ||||
| -rw-r--r-- | biology/seqkit/Makefile | 2 | ||||
| -rw-r--r-- | biology/taxonkit/Makefile | 2 | ||||
| -rw-r--r-- | biology/unikmer/Makefile | 2 |
21 files changed, 490 insertions, 135 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..f002e215a910 100644 --- a/biology/bbmap/Makefile +++ b/biology/bbmap/Makefile @@ -1,5 +1,5 @@ PORTNAME= bbmap -DISTVERSION= 39.15 +DISTVERSION= 39.33 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..c2fdad3c90f0 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 = 1753598961 +SHA256 (BBMap_39.33.tar.gz) = b82d06579e118467b5f129f06c93991196d25cc7e43cd233aeb777f85507175e +SIZE (BBMap_39.33.tar.gz) = 13433045 diff --git a/biology/bbmap/pkg-plist b/biology/bbmap/pkg-plist index 1515769118ae..9a9e248eafa3 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 +378,6 @@ 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/RefToIndex.class %%JAVAJARDIR%%/bbmap/align2/RefToIndex.java %%JAVAJARDIR%%/bbmap/align2/ReformatBatchOutput.class @@ -363,6 +390,9 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/align2/SplitMappedReads.java %%JAVAJARDIR%%/bbmap/align2/TranslateColorspaceRead.class %%JAVAJARDIR%%/bbmap/align2/TranslateColorspaceRead.java +%%JAVAJARDIR%%/bbmap/aligner/AlignRandom$1.class +%%JAVAJARDIR%%/bbmap/aligner/AlignRandom.class +%%JAVAJARDIR%%/bbmap/aligner/AlignRandom.java %%JAVAJARDIR%%/bbmap/aligner/Aligner.class %%JAVAJARDIR%%/bbmap/aligner/Aligner.java %%JAVAJARDIR%%/bbmap/aligner/Alignment.class @@ -372,10 +402,84 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/aligner/AllToAll$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$Cell.class +%%JAVAJARDIR%%/bbmap/aligner/Ksw2gg.class +%%JAVAJARDIR%%/bbmap/aligner/Ksw2gg.java +%%JAVAJARDIR%%/bbmap/aligner/KswGgJava.class +%%JAVAJARDIR%%/bbmap/aligner/KswGgJava.java +%%JAVAJARDIR%%/bbmap/aligner/MSAViz.class +%%JAVAJARDIR%%/bbmap/aligner/MSAViz.java %%JAVAJARDIR%%/bbmap/aligner/MicroAligner.class %%JAVAJARDIR%%/bbmap/aligner/MicroAligner.java %%JAVAJARDIR%%/bbmap/aligner/MicroAligner2.class @@ -384,6 +488,13 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/aligner/MicroAligner3.java %%JAVAJARDIR%%/bbmap/aligner/MicroIndex3.class %%JAVAJARDIR%%/bbmap/aligner/MicroIndex3.java +%%JAVAJARDIR%%/bbmap/aligner/MicroWrapper$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 +503,34 @@ 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/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 +547,39 @@ 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 @@ -520,40 +692,103 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/barcode/stub/PCRMatrixTile.java %%JAVAJARDIR%%/bbmap/bbmin/Minimizer.class %%JAVAJARDIR%%/bbmap/bbmin/Minimizer.java +%%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$Centroid.class +%%JAVAJARDIR%%/bbmap/bin/CrystalChamber.class +%%JAVAJARDIR%%/bbmap/bin/CrystalChamber.java %%JAVAJARDIR%%/bbmap/bin/DataLoader.class %%JAVAJARDIR%%/bbmap/bin/DataLoader.java %%JAVAJARDIR%%/bbmap/bin/FileRenamer.class %%JAVAJARDIR%%/bbmap/bin/FileRenamer.java +%%JAVAJARDIR%%/bbmap/bin/GTDBLine.class +%%JAVAJARDIR%%/bbmap/bin/GTDBLine.java +%%JAVAJARDIR%%/bbmap/bin/GeneTools.class +%%JAVAJARDIR%%/bbmap/bin/GeneTools.java +%%JAVAJARDIR%%/bbmap/bin/GradeBins$CCLine.class +%%JAVAJARDIR%%/bbmap/bin/GradeBins$ProcessThread.class +%%JAVAJARDIR%%/bbmap/bin/GradeBins.class +%%JAVAJARDIR%%/bbmap/bin/GradeBins.java +%%JAVAJARDIR%%/bbmap/bin/IDComparator.class +%%JAVAJARDIR%%/bbmap/bin/IDComparator.java +%%JAVAJARDIR%%/bbmap/bin/Key.class +%%JAVAJARDIR%%/bbmap/bin/Key.java +%%JAVAJARDIR%%/bbmap/bin/KeyValue.class +%%JAVAJARDIR%%/bbmap/bin/KeyValue.java +%%JAVAJARDIR%%/bbmap/bin/KmerProb.class +%%JAVAJARDIR%%/bbmap/bin/KmerProb.java +%%JAVAJARDIR%%/bbmap/bin/Oracle.class +%%JAVAJARDIR%%/bbmap/bin/Oracle.java %%JAVAJARDIR%%/bbmap/bin/QuickBin$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/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 @@ -928,6 +1163,8 @@ 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$1.class %%JAVAJARDIR%%/bbmap/fileIO/CopyFile.class %%JAVAJARDIR%%/bbmap/fileIO/CopyFile.java @@ -973,6 +1210,11 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/fun/DiskBench$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$Edge.class @@ -1016,6 +1258,8 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/fun/Palindrome2$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 @@ -1039,6 +1283,8 @@ 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/VcfToGff$1.class @@ -1114,49 +1360,21 @@ 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/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$LoadThread.class @@ -1189,6 +1407,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/jgi/CheckStrand.class %%JAVAJARDIR%%/bbmap/jgi/CheckStrand.java %%JAVAJARDIR%%/bbmap/jgi/CheckStrand2$ProcessThread.class +%%JAVAJARDIR%%/bbmap/jgi/CheckStrand2$Seq.class %%JAVAJARDIR%%/bbmap/jgi/CheckStrand2.class %%JAVAJARDIR%%/bbmap/jgi/CheckStrand2.java %%JAVAJARDIR%%/bbmap/jgi/Consect.class @@ -1216,9 +1435,6 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/jgi/CrisprFinder$ProcessThread.class %%JAVAJARDIR%%/bbmap/jgi/CrisprFinder.class %%JAVAJARDIR%%/bbmap/jgi/CrisprFinder.java -%%JAVAJARDIR%%/bbmap/jgi/CrossContaminate$Vessel.class -%%JAVAJARDIR%%/bbmap/jgi/CrossContaminate.class -%%JAVAJARDIR%%/bbmap/jgi/CrossContaminate.java %%JAVAJARDIR%%/bbmap/jgi/CutPrimers.class %%JAVAJARDIR%%/bbmap/jgi/CutPrimers.java %%JAVAJARDIR%%/bbmap/jgi/DecontaminateByNormalization.class @@ -1259,8 +1475,6 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/jgi/DemuxByName2.java %%JAVAJARDIR%%/bbmap/jgi/Difference.class %%JAVAJARDIR%%/bbmap/jgi/Difference.java -%%JAVAJARDIR%%/bbmap/jgi/FakeReads.class -%%JAVAJARDIR%%/bbmap/jgi/FakeReads.java %%JAVAJARDIR%%/bbmap/jgi/FilterByCoverage.class %%JAVAJARDIR%%/bbmap/jgi/FilterByCoverage.java %%JAVAJARDIR%%/bbmap/jgi/FilterBySequence$Code.class @@ -1281,8 +1495,6 @@ 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 +1535,6 @@ 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$1.class %%JAVAJARDIR%%/bbmap/jgi/MakeLengthHistogram.class %%JAVAJARDIR%%/bbmap/jgi/MakeLengthHistogram.java @@ -1336,12 +1544,6 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/jgi/MergeBarcodes.java %%JAVAJARDIR%%/bbmap/jgi/MergeSam.class %%JAVAJARDIR%%/bbmap/jgi/MergeSam.java -%%JAVAJARDIR%%/bbmap/jgi/MutateGenome$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 @@ -1357,14 +1559,14 @@ libexec/bbmap/webcheck.sh %%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 +1591,6 @@ 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$NumComparator.class @@ -1406,8 +1606,6 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/jgi/SplitSam6Way.java %%JAVAJARDIR%%/bbmap/jgi/SplitSamFile.class %%JAVAJARDIR%%/bbmap/jgi/SplitSamFile.java -%%JAVAJARDIR%%/bbmap/jgi/SynthMDA.class -%%JAVAJARDIR%%/bbmap/jgi/SynthMDA.java %%JAVAJARDIR%%/bbmap/jgi/TestFilesystem$WriteThread.class %%JAVAJARDIR%%/bbmap/jgi/TestFilesystem.class %%JAVAJARDIR%%/bbmap/jgi/TestFilesystem.java @@ -1418,6 +1616,10 @@ 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 @@ -1497,7 +1699,7 @@ 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 @@ -1526,6 +1728,8 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/ml/Profiler.java %%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 @@ -1681,8 +1885,23 @@ libexec/bbmap/webcheck.sh %%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 @@ -1719,8 +1938,16 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/shared/Primes.java %%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$1.class @@ -1770,8 +1997,6 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/sketch/Comparison.java %%JAVAJARDIR%%/bbmap/sketch/DisplayParams.class %%JAVAJARDIR%%/bbmap/sketch/DisplayParams.java -%%JAVAJARDIR%%/bbmap/sketch/GlocalAligner.class -%%JAVAJARDIR%%/bbmap/sketch/GlocalAligner.java %%JAVAJARDIR%%/bbmap/sketch/InvertKey.class %%JAVAJARDIR%%/bbmap/sketch/InvertKey.java %%JAVAJARDIR%%/bbmap/sketch/KmerLimit$ProcessThread.class @@ -2053,6 +2278,8 @@ 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 @@ -2102,6 +2329,12 @@ libexec/bbmap/webcheck.sh %%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 +2361,41 @@ 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$HashThread.class %%JAVAJARDIR%%/bbmap/tax/AccessionToTaxid.class %%JAVAJARDIR%%/bbmap/tax/AccessionToTaxid.java @@ -2139,6 +2407,8 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/tax/AnalyzeAccession.java %%JAVAJARDIR%%/bbmap/tax/AnalyzeAccession_ST.class %%JAVAJARDIR%%/bbmap/tax/AnalyzeAccession_ST.java +%%JAVAJARDIR%%/bbmap/tax/CanonicalLineage.class +%%JAVAJARDIR%%/bbmap/tax/CanonicalLineage.java %%JAVAJARDIR%%/bbmap/tax/ExplodeTree.class %%JAVAJARDIR%%/bbmap/tax/ExplodeTree.java %%JAVAJARDIR%%/bbmap/tax/FilterByTaxa.class @@ -2157,6 +2427,8 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/tax/ImgRecord.java %%JAVAJARDIR%%/bbmap/tax/ImgRecord2.class %%JAVAJARDIR%%/bbmap/tax/ImgRecord2.java +%%JAVAJARDIR%%/bbmap/tax/Lineage.class +%%JAVAJARDIR%%/bbmap/tax/Lineage.java %%JAVAJARDIR%%/bbmap/tax/PrintTaxonomy.class %%JAVAJARDIR%%/bbmap/tax/PrintTaxonomy.java %%JAVAJARDIR%%/bbmap/tax/Query.class @@ -2321,8 +2593,12 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/var/Variation.java %%JAVAJARDIR%%/bbmap/var/Varlet.class %%JAVAJARDIR%%/bbmap/var/Varlet.java +%%JAVAJARDIR%%/bbmap/var2/AnalyzeVars.class +%%JAVAJARDIR%%/bbmap/var2/AnalyzeVars.java %%JAVAJARDIR%%/bbmap/var2/ApplyVariants.class %%JAVAJARDIR%%/bbmap/var2/ApplyVariants.java +%%JAVAJARDIR%%/bbmap/var2/CVOutputWriter.class +%%JAVAJARDIR%%/bbmap/var2/CVOutputWriter.java %%JAVAJARDIR%%/bbmap/var2/CallVariants$ProcessThread.class %%JAVAJARDIR%%/bbmap/var2/CallVariants.class %%JAVAJARDIR%%/bbmap/var2/CallVariants.java @@ -2363,15 +2639,21 @@ 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 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/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/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-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 |