git: 9c42a68c3ffc - main - biology/bbmap: update 39.15 => 39.33

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From: Älven <alven_at_FreeBSD.org>
Date: Tue, 29 Jul 2025 08:03:51 UTC
The branch main has been updated by alven:

URL: https://cgit.FreeBSD.org/ports/commit/?id=9c42a68c3ffcfff62f415baf9d4e1caa2af3f44e

commit 9c42a68c3ffcfff62f415baf9d4e1caa2af3f44e
Author:     Älven <alven@FreeBSD.org>
AuthorDate: 2025-07-27 06:59:06 +0000
Commit:     Älven <alven@FreeBSD.org>
CommitDate: 2025-07-29 08:02:38 +0000

    biology/bbmap: update 39.15 => 39.33
    
    * Sort RUN_DEPENDS
    
    PR:             288480
    Approved by:    yuri@ (Mentor)
---
 biology/bbmap/Makefile  |   6 +-
 biology/bbmap/distinfo  |   6 +-
 biology/bbmap/pkg-plist | 412 ++++++++++++++++++++++++++++++++++++++++--------
 3 files changed, 353 insertions(+), 71 deletions(-)

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