git: 1f224e0bb61a - main - biology/bbmap: Update to 39.14

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From: Jason W. Bacon <jwb_at_FreeBSD.org>
Date: Mon, 13 Jan 2025 21:56:13 UTC
The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=1f224e0bb61a439d5b82958b5bbdfa2041c55c3d

commit 1f224e0bb61a439d5b82958b5bbdfa2041c55c3d
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2025-01-13 21:50:59 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2025-01-13 21:50:59 +0000

    biology/bbmap: Update to 39.14
    
    Changes: Cannot find any release notes
    
    PR:             283240
    Reported by:    alster@vinterdalen.se
---
 biology/bbmap/Makefile               |  10 +-
 biology/bbmap/distinfo               |   6 +-
 biology/bbmap/files/patch-calcmem.sh |  30 +--
 biology/bbmap/pkg-plist              | 461 +++++++++++++++++++++++++++++++----
 4 files changed, 442 insertions(+), 65 deletions(-)

diff --git a/biology/bbmap/Makefile b/biology/bbmap/Makefile
index 6807f87f5f5f..7eb55b35a9e3 100644
--- a/biology/bbmap/Makefile
+++ b/biology/bbmap/Makefile
@@ -1,12 +1,13 @@
 PORTNAME=	bbmap
-DISTVERSION=	38.92
+DISTVERSION=	39.14
 CATEGORIES=	biology java
 MASTER_SITES=	SF/bbmap/
 DISTNAME=	BBMap_${PORTVERSION}
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	BBMap short read aligner, and other bioinformatic tools
-WWW=		https://jgi.doe.gov/data-and-tools/bbtools/
+WWW=		https://jgi.doe.gov/data-and-tools/bbtools/ \
+		https://sourceforge.net/projects/bbmap/
 
 LICENSE=	BSD3CLAUSE
 LICENSE_FILE=	${WRKSRC}/license.txt
@@ -19,9 +20,10 @@ USES=		java shebangfix
 
 SHEBANG_FILES=	${WRKSRC}/*.sh
 
-WRKSRC=		${WRKDIR}/${PORTNAME}
-NO_BUILD=	yes
 NO_ARCH=	yes
+NO_BUILD=	yes
+
+WRKSRC=		${WRKDIR}/${PORTNAME}
 
 LIBEXEC_DIR=	${PREFIX}/libexec/bbmap
 
diff --git a/biology/bbmap/distinfo b/biology/bbmap/distinfo
index 391a7c547bee..c2f5a721063f 100644
--- a/biology/bbmap/distinfo
+++ b/biology/bbmap/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1629639676
-SHA256 (BBMap_38.92.tar.gz) = a5db3921684296dcbcabd0d36dc123597f587a6ac96855f4f901fee494718dc3
-SIZE (BBMap_38.92.tar.gz) = 10669924
+TIMESTAMP = 1736804942
+SHA256 (BBMap_39.14.tar.gz) = 87f7746dee28629afb368530457e7d2dfaabb4f8c5967dba4269d9a724f78e30
+SIZE (BBMap_39.14.tar.gz) = 12469315
diff --git a/biology/bbmap/files/patch-calcmem.sh b/biology/bbmap/files/patch-calcmem.sh
index db002636a860..77e676990387 100644
--- a/biology/bbmap/files/patch-calcmem.sh
+++ b/biology/bbmap/files/patch-calcmem.sh
@@ -1,10 +1,10 @@
---- calcmem.sh.orig	2021-04-13 14:05:28 UTC
+--- calcmem.sh.orig	2024-12-10 19:13:48 UTC
 +++ calcmem.sh
-@@ -72,30 +72,6 @@ function setEnvironment(){
- 	if [[ $SHIFTER_RUNTIME == 1 ]]; then
+@@ -78,26 +78,6 @@ function setEnvironment(){
+ 	if [[ "$SHIFTER_RUNTIME" = "1" ]]; then
  		#Ignore NERSC_HOST
  		shifter=1
--	elif [ -v "$EC2_HOME" ]; then
+-	elif [ -z "$EC2_HOME" ]; then
 -		#Let's assume this is the AWS taxonomy server...
 -		PATH=/test1/binaries/bgzip:$PATH
 -		PATH=/test1/binaries/lbzip2/bin:$PATH
@@ -14,20 +14,16 @@
 -	elif [ -z "$NERSC_HOST" ]; then
 -		#Not NERSC; do nothing
 -		:
+-	elif [ -z "$NERSC_HOST" ]; then
+-		#Not NERSC; do nothing
+-		:
 -	else
--		PATH=/global/projectb/sandbox/gaag/bbtools/bgzip:$PATH
--		PATH=/global/projectb/sandbox/gaag/bbtools/lbzip2/bin:$PATH
--		PATH=/global/projectb/sandbox/gaag/bbtools/sambamba:$PATH
--		PATH=/global/projectb/sandbox/gaag/bbtools/java/jdk-11.0.2/bin:$PATH
--		PATH=/global/projectb/sandbox/gaag/bbtools/pigz2/pigz-2.4:$PATH
--		
--		if [[ $NERSC_HOST == cori ]]; then
--
--			#module unload PrgEnv-intel
--			#module load PrgEnv-gnu/7.1
--			PATH=/global/projectb/sandbox/gaag/bbtools/samtools_cori/bin:$PATH
--			:
--		fi
+-		PATH=/global/cfs/cdirs/bbtools/bgzip:$PATH
+-		PATH=/global/cfs/cdirs/bbtools/lbzip2/bin:$PATH
+-                PATH=/global/cfs/cdirs/bbtools/samtools116/samtools-1.16.1:$PATH
+-		#PATH=/global/projectb/sandbox/gaag/bbtools/sambamba:$PATH
+-		PATH=/global/cfs/cdirs/bbtools/java/jdk-17/bin:$PATH
+-		PATH=/global/cfs/cdirs/bbtools/pigz2/pigz-2.4:$PATH
  	fi
  }
  
diff --git a/biology/bbmap/pkg-plist b/biology/bbmap/pkg-plist
index d4d5cbf8b549..d67fce64164a 100644
--- a/biology/bbmap/pkg-plist
+++ b/biology/bbmap/pkg-plist
@@ -6,6 +6,7 @@ bin/bloomfilter.sh
 bin/dedupe.sh
 bin/reformat.sh
 bin/tadpole.sh
+libexec/bbmap/Xcalcmem.sh
 libexec/bbmap/a_sample_mt.sh
 libexec/bbmap/addadapters.sh
 libexec/bbmap/addssu.sh
@@ -17,6 +18,7 @@ libexec/bbmap/analyzesketchresults.sh
 libexec/bbmap/applyvariants.sh
 libexec/bbmap/bbcms.sh
 libexec/bbmap/bbcountunique.sh
+libexec/bbmap/bbcrisprfinder.sh
 libexec/bbmap/bbduk.sh
 libexec/bbmap/bbest.sh
 libexec/bbmap/bbfakereads.sh
@@ -29,27 +31,35 @@ libexec/bbmap/bbnorm.sh
 libexec/bbmap/bbrealign.sh
 libexec/bbmap/bbrename.sh
 libexec/bbmap/bbsketch.sh
+libexec/bbmap/bbsort.sh
 libexec/bbmap/bbsplit.sh
 libexec/bbmap/bbsplitpairs.sh
 libexec/bbmap/bbstats.sh
 libexec/bbmap/bbversion.sh
 libexec/bbmap/bbwrap.sh
 libexec/bbmap/bloomfilter.sh
+libexec/bbmap/bloomfilterparser.sh
 libexec/bbmap/calcmem.sh
 libexec/bbmap/calctruequality.sh
 libexec/bbmap/callgenes.sh
 libexec/bbmap/callpeaks.sh
 libexec/bbmap/callvariants.sh
 libexec/bbmap/callvariants2.sh
+libexec/bbmap/cg2illumina.sh
+libexec/bbmap/checkstrand.sh
 libexec/bbmap/clumpify.sh
 libexec/bbmap/commonkmers.sh
 libexec/bbmap/comparegff.sh
+libexec/bbmap/comparelabels.sh
 libexec/bbmap/comparesketch.sh
 libexec/bbmap/comparessu.sh
 libexec/bbmap/comparevcf.sh
 libexec/bbmap/consect.sh
 libexec/bbmap/consensus.sh
+libexec/bbmap/copyfile.sh
 libexec/bbmap/countbarcodes.sh
+libexec/bbmap/countbarcodes2.sh
+libexec/bbmap/countduplicates.sh
 libexec/bbmap/countgc.sh
 libexec/bbmap/countsharedlines.sh
 libexec/bbmap/crossblock.sh
@@ -61,6 +71,7 @@ libexec/bbmap/dedupe.sh
 libexec/bbmap/dedupe2.sh
 libexec/bbmap/dedupebymapping.sh
 libexec/bbmap/demuxbyname.sh
+libexec/bbmap/demuxserver.sh
 libexec/bbmap/diskbench.sh
 libexec/bbmap/estherfilter.sh
 libexec/bbmap/explodetree.sh
@@ -78,6 +89,7 @@ libexec/bbmap/filtersam.sh
 libexec/bbmap/filtersilva.sh
 libexec/bbmap/filtersubs.sh
 libexec/bbmap/filtervcf.sh
+libexec/bbmap/findrepeats.sh
 libexec/bbmap/fixgaps.sh
 libexec/bbmap/fungalrelease.sh
 libexec/bbmap/fuse.sh
@@ -124,16 +136,24 @@ libexec/bbmap/mergesorted.sh
 libexec/bbmap/msa.sh
 libexec/bbmap/mutate.sh
 libexec/bbmap/muxbyname.sh
+libexec/bbmap/netfilter.sh
+libexec/bbmap/novademux.sh
 libexec/bbmap/partition.sh
 libexec/bbmap/phylip2fasta.sh
+libexec/bbmap/picksubset.sh
 libexec/bbmap/pileup.sh
+libexec/bbmap/pileup2.sh
 libexec/bbmap/plotflowcell.sh
 libexec/bbmap/plotgc.sh
+libexec/bbmap/plothist.sh
+libexec/bbmap/plotreadposition.sh
+libexec/bbmap/polyfilter.sh
 libexec/bbmap/postfilter.sh
 libexec/bbmap/printtime.sh
 libexec/bbmap/processfrag.sh
 libexec/bbmap/processhi-c.sh
 libexec/bbmap/processspeed.sh
+libexec/bbmap/quickbin.sh
 libexec/bbmap/randomgenome.sh
 libexec/bbmap/randomreads.sh
 libexec/bbmap/readlength.sh
@@ -156,8 +176,10 @@ libexec/bbmap/rqcfilter.sh
 libexec/bbmap/rqcfilter2.sh
 libexec/bbmap/runhmm.sh
 libexec/bbmap/samtoroc.sh
+libexec/bbmap/scoresequence.sh
 libexec/bbmap/seal.sh
 libexec/bbmap/sendsketch.sh
+libexec/bbmap/seqtovec.sh
 libexec/bbmap/shred.sh
 libexec/bbmap/shrinkaccession.sh
 libexec/bbmap/shuffle.sh
@@ -188,6 +210,7 @@ libexec/bbmap/synthmda.sh
 libexec/bbmap/tadpipe.sh
 libexec/bbmap/tadpole.sh
 libexec/bbmap/tadwrapper.sh
+libexec/bbmap/tagandmerge.sh
 libexec/bbmap/taxonomy.sh
 libexec/bbmap/taxserver.sh
 libexec/bbmap/taxsize.sh
@@ -197,7 +220,10 @@ libexec/bbmap/testformat.sh
 libexec/bbmap/testformat2.sh
 libexec/bbmap/tetramerfreq.sh
 libexec/bbmap/textfile.sh
+libexec/bbmap/tiledump.sh
+libexec/bbmap/train.sh
 libexec/bbmap/translate6frames.sh
+libexec/bbmap/trimcontigs.sh
 libexec/bbmap/unicode2ascii.sh
 libexec/bbmap/unzip.sh
 libexec/bbmap/vcf2gff.sh
@@ -350,6 +376,14 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/aligner/FlatAligner.java
 %%JAVAJARDIR%%/bbmap/aligner/FlatAligner2.class
 %%JAVAJARDIR%%/bbmap/aligner/FlatAligner2.java
+%%JAVAJARDIR%%/bbmap/aligner/MicroAligner.class
+%%JAVAJARDIR%%/bbmap/aligner/MicroAligner.java
+%%JAVAJARDIR%%/bbmap/aligner/MicroAligner2.class
+%%JAVAJARDIR%%/bbmap/aligner/MicroAligner2.java
+%%JAVAJARDIR%%/bbmap/aligner/MicroAligner3.class
+%%JAVAJARDIR%%/bbmap/aligner/MicroAligner3.java
+%%JAVAJARDIR%%/bbmap/aligner/MicroIndex3.class
+%%JAVAJARDIR%%/bbmap/aligner/MicroIndex3.java
 %%JAVAJARDIR%%/bbmap/aligner/MultiStateAligner9PacBioAdapter.class
 %%JAVAJARDIR%%/bbmap/aligner/MultiStateAligner9PacBioAdapter.java
 %%JAVAJARDIR%%/bbmap/aligner/MultiStateAligner9PacBioAdapter2.class
@@ -358,6 +392,8 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/aligner/MultiStateAligner9PacBioAdapter3.java
 %%JAVAJARDIR%%/bbmap/aligner/MultiStateAligner9PacBioAdapter_WithBarriers.class
 %%JAVAJARDIR%%/bbmap/aligner/MultiStateAligner9PacBioAdapter_WithBarriers.java
+%%JAVAJARDIR%%/bbmap/aligner/SideChannel3.class
+%%JAVAJARDIR%%/bbmap/aligner/SideChannel3.java
 %%JAVAJARDIR%%/bbmap/aligner/SingleStateAlignerFlat.class
 %%JAVAJARDIR%%/bbmap/aligner/SingleStateAlignerFlat.java
 %%JAVAJARDIR%%/bbmap/aligner/SingleStateAlignerFlat2.class
@@ -430,6 +466,84 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/assemble/TadpoleWrapper$Record.class
 %%JAVAJARDIR%%/bbmap/assemble/TadpoleWrapper.class
 %%JAVAJARDIR%%/bbmap/assemble/TadpoleWrapper.java
+%%JAVAJARDIR%%/bbmap/barcode/AnalyzeBarcodes.class
+%%JAVAJARDIR%%/bbmap/barcode/AnalyzeBarcodes.java
+%%JAVAJARDIR%%/bbmap/barcode/Barcode.class
+%%JAVAJARDIR%%/bbmap/barcode/Barcode.java
+%%JAVAJARDIR%%/bbmap/barcode/BarcodeCounter.class
+%%JAVAJARDIR%%/bbmap/barcode/BarcodeCounter.java
+%%JAVAJARDIR%%/bbmap/barcode/BarcodeMappingStats.class
+%%JAVAJARDIR%%/bbmap/barcode/BarcodeMappingStats.java
+%%JAVAJARDIR%%/bbmap/barcode/BarcodeStats.class
+%%JAVAJARDIR%%/bbmap/barcode/BarcodeStats.java
+%%JAVAJARDIR%%/bbmap/barcode/CompareLabels$Label.class
+%%JAVAJARDIR%%/bbmap/barcode/CompareLabels.class
+%%JAVAJARDIR%%/bbmap/barcode/CompareLabels.java
+%%JAVAJARDIR%%/bbmap/barcode/CorrelateBarcodes.class
+%%JAVAJARDIR%%/bbmap/barcode/CorrelateBarcodes.java
+%%JAVAJARDIR%%/bbmap/barcode/CountBarcodes.class
+%%JAVAJARDIR%%/bbmap/barcode/CountBarcodes.java
+%%JAVAJARDIR%%/bbmap/barcode/CountBarcodes2.class
+%%JAVAJARDIR%%/bbmap/barcode/CountBarcodes2.java
+%%JAVAJARDIR%%/bbmap/barcode/DemuxClient.class
+%%JAVAJARDIR%%/bbmap/barcode/DemuxClient.java
+%%JAVAJARDIR%%/bbmap/barcode/DemuxData.class
+%%JAVAJARDIR%%/bbmap/barcode/DemuxData.java
+%%JAVAJARDIR%%/bbmap/barcode/DemuxServer$BaseHandler.class
+%%JAVAJARDIR%%/bbmap/barcode/DemuxServer$DemuxHandler.class
+%%JAVAJARDIR%%/bbmap/barcode/DemuxServer$IconHandler.class
+%%JAVAJARDIR%%/bbmap/barcode/DemuxServer$KillHandler.class
+%%JAVAJARDIR%%/bbmap/barcode/DemuxServer$Pair.class
+%%JAVAJARDIR%%/bbmap/barcode/DemuxServer$StatsHandler.class
+%%JAVAJARDIR%%/bbmap/barcode/DemuxServer.class
+%%JAVAJARDIR%%/bbmap/barcode/DemuxServer.java
+%%JAVAJARDIR%%/bbmap/barcode/LegacyFileWriter$QTag.class
+%%JAVAJARDIR%%/bbmap/barcode/LegacyFileWriter.class
+%%JAVAJARDIR%%/bbmap/barcode/LegacyFileWriter.java
+%%JAVAJARDIR%%/bbmap/barcode/NovaDemux.class
+%%JAVAJARDIR%%/bbmap/barcode/NovaDemux.java
+%%JAVAJARDIR%%/bbmap/barcode/PCRMatrix$MapLine.class
+%%JAVAJARDIR%%/bbmap/barcode/PCRMatrix.class
+%%JAVAJARDIR%%/bbmap/barcode/PCRMatrix.java
+%%JAVAJARDIR%%/bbmap/barcode/PCRMatrixHDist$PopThread.class
+%%JAVAJARDIR%%/bbmap/barcode/PCRMatrixHDist.class
+%%JAVAJARDIR%%/bbmap/barcode/PCRMatrixHDist.java
+%%JAVAJARDIR%%/bbmap/barcode/TagAndMerge.class
+%%JAVAJARDIR%%/bbmap/barcode/TagAndMerge.java
+%%JAVAJARDIR%%/bbmap/barcode/Transition.class
+%%JAVAJARDIR%%/bbmap/barcode/Transition.java
+%%JAVAJARDIR%%/bbmap/barcode/stub/PCRMatrixProb.class
+%%JAVAJARDIR%%/bbmap/barcode/stub/PCRMatrixProb.java
+%%JAVAJARDIR%%/bbmap/barcode/stub/PCRMatrixProbAbstract.class
+%%JAVAJARDIR%%/bbmap/barcode/stub/PCRMatrixProbAbstract.java
+%%JAVAJARDIR%%/bbmap/barcode/stub/PCRMatrixTile.class
+%%JAVAJARDIR%%/bbmap/barcode/stub/PCRMatrixTile.java
+%%JAVAJARDIR%%/bbmap/bbmin/Minimizer.class
+%%JAVAJARDIR%%/bbmap/bbmin/Minimizer.java
+%%JAVAJARDIR%%/bbmap/bin/Bin.class
+%%JAVAJARDIR%%/bbmap/bin/Bin.java
+%%JAVAJARDIR%%/bbmap/bin/BinObject.class
+%%JAVAJARDIR%%/bbmap/bin/BinObject.java
+%%JAVAJARDIR%%/bbmap/bin/BinSketcher$ProcessThread.class
+%%JAVAJARDIR%%/bbmap/bin/BinSketcher.class
+%%JAVAJARDIR%%/bbmap/bin/BinSketcher.java
+%%JAVAJARDIR%%/bbmap/bin/Binner.class
+%%JAVAJARDIR%%/bbmap/bin/Binner.java
+%%JAVAJARDIR%%/bbmap/bin/Cluster.class
+%%JAVAJARDIR%%/bbmap/bin/Cluster.java
+%%JAVAJARDIR%%/bbmap/bin/Contig.class
+%%JAVAJARDIR%%/bbmap/bin/Contig.java
+%%JAVAJARDIR%%/bbmap/bin/DataLoader.class
+%%JAVAJARDIR%%/bbmap/bin/DataLoader.java
+%%JAVAJARDIR%%/bbmap/bin/QuickBin$ProcessThread.class
+%%JAVAJARDIR%%/bbmap/bin/QuickBin.class
+%%JAVAJARDIR%%/bbmap/bin/QuickBin.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/bloom/BloomFilter.class
 %%JAVAJARDIR%%/bbmap/bloom/BloomFilter.java
 %%JAVAJARDIR%%/bbmap/bloom/BloomFilterCorrector.class
@@ -443,6 +557,9 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/bloom/ErrorCorrect$1.class
 %%JAVAJARDIR%%/bbmap/bloom/ErrorCorrect.class
 %%JAVAJARDIR%%/bbmap/bloom/ErrorCorrect.java
+%%JAVAJARDIR%%/bbmap/bloom/IndexCounter$CountThread.class
+%%JAVAJARDIR%%/bbmap/bloom/IndexCounter.class
+%%JAVAJARDIR%%/bbmap/bloom/IndexCounter.java
 %%JAVAJARDIR%%/bbmap/bloom/KCountArray$AllocThread.class
 %%JAVAJARDIR%%/bbmap/bloom/KCountArray.class
 %%JAVAJARDIR%%/bbmap/bloom/KCountArray.java
@@ -478,23 +595,25 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/bloom/KmerCount5.java
 %%JAVAJARDIR%%/bbmap/bloom/KmerCount6.class
 %%JAVAJARDIR%%/bbmap/bloom/KmerCount6.java
-%%JAVAJARDIR%%/bbmap/bloom/KmerCount6MT$CountThread.class
-%%JAVAJARDIR%%/bbmap/bloom/KmerCount6MT.class
-%%JAVAJARDIR%%/bbmap/bloom/KmerCount6MT.java
-%%JAVAJARDIR%%/bbmap/bloom/KmerCount7MT$CountThread.class
-%%JAVAJARDIR%%/bbmap/bloom/KmerCount7MT.class
-%%JAVAJARDIR%%/bbmap/bloom/KmerCount7MT.java
-%%JAVAJARDIR%%/bbmap/bloom/KmerCount7MTA$1.class
-%%JAVAJARDIR%%/bbmap/bloom/KmerCount7MTA$CountThread.class
-%%JAVAJARDIR%%/bbmap/bloom/KmerCount7MTA$CountThread2.class
-%%JAVAJARDIR%%/bbmap/bloom/KmerCount7MTA.class
-%%JAVAJARDIR%%/bbmap/bloom/KmerCount7MTA.java
 %%JAVAJARDIR%%/bbmap/bloom/KmerCountAbstract.class
 %%JAVAJARDIR%%/bbmap/bloom/KmerCountAbstract.java
 %%JAVAJARDIR%%/bbmap/bloom/LargeKmerCount.class
 %%JAVAJARDIR%%/bbmap/bloom/LargeKmerCount.java
 %%JAVAJARDIR%%/bbmap/bloom/LargeKmerCount2.class
 %%JAVAJARDIR%%/bbmap/bloom/LargeKmerCount2.java
+%%JAVAJARDIR%%/bbmap/bloom/ParseBloomFilter.class
+%%JAVAJARDIR%%/bbmap/bloom/ParseBloomFilter.java
+%%JAVAJARDIR%%/bbmap/bloom/PolyFilter$ProcessThread.class
+%%JAVAJARDIR%%/bbmap/bloom/PolyFilter.class
+%%JAVAJARDIR%%/bbmap/bloom/PolyFilter.java
+%%JAVAJARDIR%%/bbmap/bloom/ReadCounter$1.class
+%%JAVAJARDIR%%/bbmap/bloom/ReadCounter$CountThread.class
+%%JAVAJARDIR%%/bbmap/bloom/ReadCounter.class
+%%JAVAJARDIR%%/bbmap/bloom/ReadCounter.java
+%%JAVAJARDIR%%/bbmap/bloom/ReadCounter_old$1.class
+%%JAVAJARDIR%%/bbmap/bloom/ReadCounter_old$CountThread.class
+%%JAVAJARDIR%%/bbmap/bloom/ReadCounter_old.class
+%%JAVAJARDIR%%/bbmap/bloom/ReadCounter_old.java
 %%JAVAJARDIR%%/bbmap/bloom/TestLargeKmer.class
 %%JAVAJARDIR%%/bbmap/bloom/TestLargeKmer.java
 %%JAVAJARDIR%%/bbmap/cardinality/BBLog.class
@@ -532,6 +651,8 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/clump/ClumpTools.java
 %%JAVAJARDIR%%/bbmap/clump/Clumpify.class
 %%JAVAJARDIR%%/bbmap/clump/Clumpify.java
+%%JAVAJARDIR%%/bbmap/clump/Hasher.class
+%%JAVAJARDIR%%/bbmap/clump/Hasher.java
 %%JAVAJARDIR%%/bbmap/clump/KmerComparator$HashThread.class
 %%JAVAJARDIR%%/bbmap/clump/KmerComparator.class
 %%JAVAJARDIR%%/bbmap/clump/KmerComparator.java
@@ -756,6 +877,9 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/driver/SummarizeQuast$QuastSummary.class
 %%JAVAJARDIR%%/bbmap/driver/SummarizeQuast.class
 %%JAVAJARDIR%%/bbmap/driver/SummarizeQuast.java
+%%JAVAJARDIR%%/bbmap/driver/SummarizeSealCrosstalk$Result.class
+%%JAVAJARDIR%%/bbmap/driver/SummarizeSealCrosstalk.class
+%%JAVAJARDIR%%/bbmap/driver/SummarizeSealCrosstalk.java
 %%JAVAJARDIR%%/bbmap/driver/SummarizeSealStats$SealSummary.class
 %%JAVAJARDIR%%/bbmap/driver/SummarizeSealStats.class
 %%JAVAJARDIR%%/bbmap/driver/SummarizeSealStats.java
@@ -833,15 +957,37 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/fun/Calc.java
 %%JAVAJARDIR%%/bbmap/fun/Chance.class
 %%JAVAJARDIR%%/bbmap/fun/Chance.java
+%%JAVAJARDIR%%/bbmap/fun/Crunch.class
+%%JAVAJARDIR%%/bbmap/fun/Crunch.java
 %%JAVAJARDIR%%/bbmap/fun/DiskBench$ReadThread.class
 %%JAVAJARDIR%%/bbmap/fun/DiskBench$WriteThread.class
 %%JAVAJARDIR%%/bbmap/fun/DiskBench.class
 %%JAVAJARDIR%%/bbmap/fun/DiskBench.java
+%%JAVAJARDIR%%/bbmap/fun/Dongle.class
+%%JAVAJARDIR%%/bbmap/fun/Dongle.java
 %%JAVAJARDIR%%/bbmap/fun/FindPath$Edge.class
 %%JAVAJARDIR%%/bbmap/fun/FindPath$Node.class
 %%JAVAJARDIR%%/bbmap/fun/FindPath$Path.class
 %%JAVAJARDIR%%/bbmap/fun/FindPath.class
 %%JAVAJARDIR%%/bbmap/fun/FindPath.java
+%%JAVAJARDIR%%/bbmap/fun/Foo.class
+%%JAVAJARDIR%%/bbmap/fun/Foo.java
+%%JAVAJARDIR%%/bbmap/fun/Foo2.class
+%%JAVAJARDIR%%/bbmap/fun/Foo2.java
+%%JAVAJARDIR%%/bbmap/fun/Foo3$LongList.class
+%%JAVAJARDIR%%/bbmap/fun/Foo3$Pair.class
+%%JAVAJARDIR%%/bbmap/fun/Foo3.class
+%%JAVAJARDIR%%/bbmap/fun/Foo3.java
+%%JAVAJARDIR%%/bbmap/fun/Foo4$Pair.class
+%%JAVAJARDIR%%/bbmap/fun/Foo4.class
+%%JAVAJARDIR%%/bbmap/fun/Foo4.java
+%%JAVAJARDIR%%/bbmap/fun/Foo5$LongList.class
+%%JAVAJARDIR%%/bbmap/fun/Foo5.class
+%%JAVAJARDIR%%/bbmap/fun/Foo5.java
+%%JAVAJARDIR%%/bbmap/fun/Foo6.class
+%%JAVAJARDIR%%/bbmap/fun/Foo6.java
+%%JAVAJARDIR%%/bbmap/fun/Foo7.class
+%%JAVAJARDIR%%/bbmap/fun/Foo7.java
 %%JAVAJARDIR%%/bbmap/fun/Genetic$Bug.class
 %%JAVAJARDIR%%/bbmap/fun/Genetic.class
 %%JAVAJARDIR%%/bbmap/fun/Genetic.java
@@ -850,8 +996,16 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/fun/MakeAdjacencyList$1.class
 %%JAVAJARDIR%%/bbmap/fun/MakeAdjacencyList.class
 %%JAVAJARDIR%%/bbmap/fun/MakeAdjacencyList.java
+%%JAVAJARDIR%%/bbmap/fun/Merced$Person.class
+%%JAVAJARDIR%%/bbmap/fun/Merced.class
+%%JAVAJARDIR%%/bbmap/fun/Merced.java
+%%JAVAJARDIR%%/bbmap/fun/PalSim.class
+%%JAVAJARDIR%%/bbmap/fun/PalSim.java
 %%JAVAJARDIR%%/bbmap/fun/Palindrome.class
 %%JAVAJARDIR%%/bbmap/fun/Palindrome.java
+%%JAVAJARDIR%%/bbmap/fun/Palindrome2$Drome.class
+%%JAVAJARDIR%%/bbmap/fun/Palindrome2.class
+%%JAVAJARDIR%%/bbmap/fun/Palindrome2.java
 %%JAVAJARDIR%%/bbmap/fun/ProbShared.class
 %%JAVAJARDIR%%/bbmap/fun/ProbShared.java
 %%JAVAJARDIR%%/bbmap/fun/ProbShared2.class
@@ -875,27 +1029,48 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/gff/GbffLocus.java
 %%JAVAJARDIR%%/bbmap/gff/GffLine.class
 %%JAVAJARDIR%%/bbmap/gff/GffLine.java
+%%JAVAJARDIR%%/bbmap/gff/ParseCrispr.class
+%%JAVAJARDIR%%/bbmap/gff/ParseCrispr.java
 %%JAVAJARDIR%%/bbmap/gff/VcfToGff$1.class
 %%JAVAJARDIR%%/bbmap/gff/VcfToGff.class
 %%JAVAJARDIR%%/bbmap/gff/VcfToGff.java
+%%JAVAJARDIR%%/bbmap/hiseq/AnalyzeFlowCell$ProcessThread.class
 %%JAVAJARDIR%%/bbmap/hiseq/AnalyzeFlowCell.class
 %%JAVAJARDIR%%/bbmap/hiseq/AnalyzeFlowCell.java
+%%JAVAJARDIR%%/bbmap/hiseq/BGI2Illumina.class
+%%JAVAJARDIR%%/bbmap/hiseq/BGI2Illumina.java
+%%JAVAJARDIR%%/bbmap/hiseq/BGIHeaderParser.class
+%%JAVAJARDIR%%/bbmap/hiseq/BGIHeaderParser.java
+%%JAVAJARDIR%%/bbmap/hiseq/BGIHeaderParser2.class
+%%JAVAJARDIR%%/bbmap/hiseq/BGIHeaderParser2.java
 %%JAVAJARDIR%%/bbmap/hiseq/CycleTracker.class
 %%JAVAJARDIR%%/bbmap/hiseq/CycleTracker.java
 %%JAVAJARDIR%%/bbmap/hiseq/FlowCell.class
 %%JAVAJARDIR%%/bbmap/hiseq/FlowCell.java
 %%JAVAJARDIR%%/bbmap/hiseq/FlowcellCoordinate.class
 %%JAVAJARDIR%%/bbmap/hiseq/FlowcellCoordinate.java
-%%JAVAJARDIR%%/bbmap/hiseq/IlluminaHeaderParser.class
-%%JAVAJARDIR%%/bbmap/hiseq/IlluminaHeaderParser.java
+%%JAVAJARDIR%%/bbmap/hiseq/IlluminaHeaderParser1.class
+%%JAVAJARDIR%%/bbmap/hiseq/IlluminaHeaderParser1.java
+%%JAVAJARDIR%%/bbmap/hiseq/IlluminaHeaderParser2.class
+%%JAVAJARDIR%%/bbmap/hiseq/IlluminaHeaderParser2.java
+%%JAVAJARDIR%%/bbmap/hiseq/Lane$TileIterator.class
 %%JAVAJARDIR%%/bbmap/hiseq/Lane.class
 %%JAVAJARDIR%%/bbmap/hiseq/Lane.java
 %%JAVAJARDIR%%/bbmap/hiseq/MicroTile.class
 %%JAVAJARDIR%%/bbmap/hiseq/MicroTile.java
+%%JAVAJARDIR%%/bbmap/hiseq/PlotFlowCell$WorkerThread.class
 %%JAVAJARDIR%%/bbmap/hiseq/PlotFlowCell.class
 %%JAVAJARDIR%%/bbmap/hiseq/PlotFlowCell.java
+%%JAVAJARDIR%%/bbmap/hiseq/PlotHist.class
+%%JAVAJARDIR%%/bbmap/hiseq/PlotHist.java
+%%JAVAJARDIR%%/bbmap/hiseq/PlotReadPosition.class
+%%JAVAJARDIR%%/bbmap/hiseq/PlotReadPosition.java
+%%JAVAJARDIR%%/bbmap/hiseq/ReadHeaderParser.class
+%%JAVAJARDIR%%/bbmap/hiseq/ReadHeaderParser.java
 %%JAVAJARDIR%%/bbmap/hiseq/Tile.class
 %%JAVAJARDIR%%/bbmap/hiseq/Tile.java
+%%JAVAJARDIR%%/bbmap/hiseq/TileDump.class
+%%JAVAJARDIR%%/bbmap/hiseq/TileDump.java
 %%JAVAJARDIR%%/bbmap/hmm/HMMSearchLine.class
 %%JAVAJARDIR%%/bbmap/hmm/HMMSearchLine.java
 %%JAVAJARDIR%%/bbmap/hmm/HMMSearchReport.class
@@ -978,10 +1153,6 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/jgi/BBDuk$ProcessThread.class
 %%JAVAJARDIR%%/bbmap/jgi/BBDuk.class
 %%JAVAJARDIR%%/bbmap/jgi/BBDuk.java
-%%JAVAJARDIR%%/bbmap/jgi/BBDuk2$LoadThread.class
-%%JAVAJARDIR%%/bbmap/jgi/BBDuk2$ProcessThread.class
-%%JAVAJARDIR%%/bbmap/jgi/BBDuk2.class
-%%JAVAJARDIR%%/bbmap/jgi/BBDuk2.java
 %%JAVAJARDIR%%/bbmap/jgi/BBMask$MaskLowEntropyThread.class
 %%JAVAJARDIR%%/bbmap/jgi/BBMask$MaskRepeatThread.class
 %%JAVAJARDIR%%/bbmap/jgi/BBMask$MaskSamThread.class
@@ -1005,12 +1176,19 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/jgi/CallPeaks$Peak.class
 %%JAVAJARDIR%%/bbmap/jgi/CallPeaks.class
 %%JAVAJARDIR%%/bbmap/jgi/CallPeaks.java
+%%JAVAJARDIR%%/bbmap/jgi/CheckStrand.class
+%%JAVAJARDIR%%/bbmap/jgi/CheckStrand.java
+%%JAVAJARDIR%%/bbmap/jgi/CheckStrand2$ProcessThread.class
+%%JAVAJARDIR%%/bbmap/jgi/CheckStrand2.class
+%%JAVAJARDIR%%/bbmap/jgi/CheckStrand2.java
 %%JAVAJARDIR%%/bbmap/jgi/Consect.class
 %%JAVAJARDIR%%/bbmap/jgi/Consect.java
-%%JAVAJARDIR%%/bbmap/jgi/CorrelateBarcodes.class
-%%JAVAJARDIR%%/bbmap/jgi/CorrelateBarcodes.java
-%%JAVAJARDIR%%/bbmap/jgi/CountBarcodes.class
-%%JAVAJARDIR%%/bbmap/jgi/CountBarcodes.java
+%%JAVAJARDIR%%/bbmap/jgi/CountDuplicates$ProcessThread.class
+%%JAVAJARDIR%%/bbmap/jgi/CountDuplicates.class
+%%JAVAJARDIR%%/bbmap/jgi/CountDuplicates.java
+%%JAVAJARDIR%%/bbmap/jgi/CountDuplicatesBuffered$ProcessThread.class
+%%JAVAJARDIR%%/bbmap/jgi/CountDuplicatesBuffered.class
+%%JAVAJARDIR%%/bbmap/jgi/CountDuplicatesBuffered.java
 %%JAVAJARDIR%%/bbmap/jgi/CountGC$1.class
 %%JAVAJARDIR%%/bbmap/jgi/CountGC.class
 %%JAVAJARDIR%%/bbmap/jgi/CountGC.java
@@ -1020,6 +1198,14 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/jgi/CovStatsLine.java
 %%JAVAJARDIR%%/bbmap/jgi/CoveragePileup.class
 %%JAVAJARDIR%%/bbmap/jgi/CoveragePileup.java
+%%JAVAJARDIR%%/bbmap/jgi/CoveragePileupMT$LoadThread.class
+%%JAVAJARDIR%%/bbmap/jgi/CoveragePileupMT.class
+%%JAVAJARDIR%%/bbmap/jgi/CoveragePileupMT.java
+%%JAVAJARDIR%%/bbmap/jgi/CrisprFinder$1.class
+%%JAVAJARDIR%%/bbmap/jgi/CrisprFinder$Alignment.class
+%%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
@@ -1148,10 +1334,15 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/jgi/MutateGenome2.java
 %%JAVAJARDIR%%/bbmap/jgi/Orf.class
 %%JAVAJARDIR%%/bbmap/jgi/Orf.java
+%%JAVAJARDIR%%/bbmap/jgi/PartitionReads$Partition.class
 %%JAVAJARDIR%%/bbmap/jgi/PartitionReads.class
 %%JAVAJARDIR%%/bbmap/jgi/PartitionReads.java
 %%JAVAJARDIR%%/bbmap/jgi/PhylipToFasta.class
 %%JAVAJARDIR%%/bbmap/jgi/PhylipToFasta.java
+%%JAVAJARDIR%%/bbmap/jgi/PickSubset$Edge.class
+%%JAVAJARDIR%%/bbmap/jgi/PickSubset$Node.class
+%%JAVAJARDIR%%/bbmap/jgi/PickSubset.class
+%%JAVAJARDIR%%/bbmap/jgi/PickSubset.java
 %%JAVAJARDIR%%/bbmap/jgi/RQCFilter2.class
 %%JAVAJARDIR%%/bbmap/jgi/RQCFilter2.java
 %%JAVAJARDIR%%/bbmap/jgi/RQCFilterStats.class
@@ -1205,14 +1396,11 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/jgi/SplitSam6Way.java
 %%JAVAJARDIR%%/bbmap/jgi/SplitSamFile.class
 %%JAVAJARDIR%%/bbmap/jgi/SplitSamFile.java
-%%JAVAJARDIR%%/bbmap/jgi/StringCount.class
-%%JAVAJARDIR%%/bbmap/jgi/StringCount.java
 %%JAVAJARDIR%%/bbmap/jgi/SynthMDA.class
 %%JAVAJARDIR%%/bbmap/jgi/SynthMDA.java
 %%JAVAJARDIR%%/bbmap/jgi/TestFilesystem$WriteThread.class
 %%JAVAJARDIR%%/bbmap/jgi/TestFilesystem.class
 %%JAVAJARDIR%%/bbmap/jgi/TestFilesystem.java
-%%JAVAJARDIR%%/bbmap/jgi/TestFormat$Barcode.class
 %%JAVAJARDIR%%/bbmap/jgi/TestFormat$TestThread.class
 %%JAVAJARDIR%%/bbmap/jgi/TestFormat.class
 %%JAVAJARDIR%%/bbmap/jgi/TestFormat.java
@@ -1222,6 +1410,9 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/jgi/TetramerFrequencies.java
 %%JAVAJARDIR%%/bbmap/jgi/TranslateSixFrames.class
 %%JAVAJARDIR%%/bbmap/jgi/TranslateSixFrames.java
+%%JAVAJARDIR%%/bbmap/jgi/TrimContigs$Range.class
+%%JAVAJARDIR%%/bbmap/jgi/TrimContigs.class
+%%JAVAJARDIR%%/bbmap/jgi/TrimContigs.java
 %%JAVAJARDIR%%/bbmap/jgi/UnicodeToAscii.class
 %%JAVAJARDIR%%/bbmap/jgi/UnicodeToAscii.java
 %%JAVAJARDIR%%/bbmap/jgi/Unzip.class
@@ -1277,6 +1468,8 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/kmer/OwnershipThread.java
 %%JAVAJARDIR%%/bbmap/kmer/ScheduleMaker.class
 %%JAVAJARDIR%%/bbmap/kmer/ScheduleMaker.java
+%%JAVAJARDIR%%/bbmap/kmer/SimpleKmerTable.class
+%%JAVAJARDIR%%/bbmap/kmer/SimpleKmerTable.java
 %%JAVAJARDIR%%/bbmap/kmer/TableLoaderLockFree$LoadThread.class
 %%JAVAJARDIR%%/bbmap/kmer/TableLoaderLockFree.class
 %%JAVAJARDIR%%/bbmap/kmer/TableLoaderLockFree.java
@@ -1284,9 +1477,82 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/kmer/TableReader.java
 %%JAVAJARDIR%%/bbmap/kmer/Walker.class
 %%JAVAJARDIR%%/bbmap/kmer/Walker.java
+%%JAVAJARDIR%%/bbmap/ml/Bell.class
+%%JAVAJARDIR%%/bbmap/ml/Bell.java
+%%JAVAJARDIR%%/bbmap/ml/Cell.class
+%%JAVAJARDIR%%/bbmap/ml/Cell.java
+%%JAVAJARDIR%%/bbmap/ml/CellNet.class
+%%JAVAJARDIR%%/bbmap/ml/CellNet.java
+%%JAVAJARDIR%%/bbmap/ml/CellNetParser.class
+%%JAVAJARDIR%%/bbmap/ml/CellNetParser.java
+%%JAVAJARDIR%%/bbmap/ml/CellNetReverseComparator.class
+%%JAVAJARDIR%%/bbmap/ml/CellNetReverseComparator.java
+%%JAVAJARDIR%%/bbmap/ml/DataLoader$Pair.class
+%%JAVAJARDIR%%/bbmap/ml/DataLoader.class
+%%JAVAJARDIR%%/bbmap/ml/DataLoader.java
+%%JAVAJARDIR%%/bbmap/ml/ExtendedMSig.class
+%%JAVAJARDIR%%/bbmap/ml/ExtendedMSig.java
+%%JAVAJARDIR%%/bbmap/ml/ExtendedSigmoid.class
+%%JAVAJARDIR%%/bbmap/ml/ExtendedSigmoid.java
+%%JAVAJARDIR%%/bbmap/ml/Function.class
+%%JAVAJARDIR%%/bbmap/ml/Function.java
+%%JAVAJARDIR%%/bbmap/ml/Functions.class
+%%JAVAJARDIR%%/bbmap/ml/Functions.java
+%%JAVAJARDIR%%/bbmap/ml/JobData.class
+%%JAVAJARDIR%%/bbmap/ml/JobData.java
+%%JAVAJARDIR%%/bbmap/ml/JobResults.class
+%%JAVAJARDIR%%/bbmap/ml/JobResults.java
+%%JAVAJARDIR%%/bbmap/ml/MSig.class
+%%JAVAJARDIR%%/bbmap/ml/MSig.java
+%%JAVAJARDIR%%/bbmap/ml/Matrix.class
+%%JAVAJARDIR%%/bbmap/ml/Matrix.java
+%%JAVAJARDIR%%/bbmap/ml/NetFilter$ProcessThread.class
+%%JAVAJARDIR%%/bbmap/ml/NetFilter.class
+%%JAVAJARDIR%%/bbmap/ml/NetFilter.java
 %%JAVAJARDIR%%/bbmap/ml/ProcessBBMergeHeaders$Header.class
 %%JAVAJARDIR%%/bbmap/ml/ProcessBBMergeHeaders.class
 %%JAVAJARDIR%%/bbmap/ml/ProcessBBMergeHeaders.java
+%%JAVAJARDIR%%/bbmap/ml/Profiler.class
+%%JAVAJARDIR%%/bbmap/ml/Profiler.java
+%%JAVAJARDIR%%/bbmap/ml/RSLog.class
+%%JAVAJARDIR%%/bbmap/ml/RSLog.java
+%%JAVAJARDIR%%/bbmap/ml/Sample.class
+%%JAVAJARDIR%%/bbmap/ml/Sample.java
+%%JAVAJARDIR%%/bbmap/ml/SampleErrorComparator.class
+%%JAVAJARDIR%%/bbmap/ml/SampleErrorComparator.java
+%%JAVAJARDIR%%/bbmap/ml/SampleSet.class
+%%JAVAJARDIR%%/bbmap/ml/SampleSet.java
+%%JAVAJARDIR%%/bbmap/ml/SampleValueComparator.class
+%%JAVAJARDIR%%/bbmap/ml/SampleValueComparator.java
+%%JAVAJARDIR%%/bbmap/ml/ScannerThread$LaunchThread.class
+%%JAVAJARDIR%%/bbmap/ml/ScannerThread.class
+%%JAVAJARDIR%%/bbmap/ml/ScannerThread.java
+%%JAVAJARDIR%%/bbmap/ml/ScoreSequence.class
+%%JAVAJARDIR%%/bbmap/ml/ScoreSequence.java
+%%JAVAJARDIR%%/bbmap/ml/Seed.class
+%%JAVAJARDIR%%/bbmap/ml/Seed.java
+%%JAVAJARDIR%%/bbmap/ml/SequenceToVector$1.class
+%%JAVAJARDIR%%/bbmap/ml/SequenceToVector.class
+%%JAVAJARDIR%%/bbmap/ml/SequenceToVector.java
+%%JAVAJARDIR%%/bbmap/ml/Sigmoid.class
+%%JAVAJARDIR%%/bbmap/ml/Sigmoid.java
+%%JAVAJARDIR%%/bbmap/ml/Source.class
+%%JAVAJARDIR%%/bbmap/ml/Source.java
+%%JAVAJARDIR%%/bbmap/ml/Status.class
+%%JAVAJARDIR%%/bbmap/ml/Status.java
+%%JAVAJARDIR%%/bbmap/ml/Subset.class
+%%JAVAJARDIR%%/bbmap/ml/Subset.java
+%%JAVAJARDIR%%/bbmap/ml/Swish.class
+%%JAVAJARDIR%%/bbmap/ml/Swish.java
+%%JAVAJARDIR%%/bbmap/ml/Tanh.class
+%%JAVAJARDIR%%/bbmap/ml/Tanh.java
+%%JAVAJARDIR%%/bbmap/ml/Trainer.class
+%%JAVAJARDIR%%/bbmap/ml/Trainer.java
+%%JAVAJARDIR%%/bbmap/ml/TrainerThread$LaunchThread.class
+%%JAVAJARDIR%%/bbmap/ml/TrainerThread.class
+%%JAVAJARDIR%%/bbmap/ml/TrainerThread.java
+%%JAVAJARDIR%%/bbmap/ml/WorkerThread.class
+%%JAVAJARDIR%%/bbmap/ml/WorkerThread.java
 %%JAVAJARDIR%%/bbmap/pacbio/CalcCoverageFromSites$1.class
 %%JAVAJARDIR%%/bbmap/pacbio/CalcCoverageFromSites.class
 %%JAVAJARDIR%%/bbmap/pacbio/CalcCoverageFromSites.java
@@ -1339,9 +1605,6 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/prok/CallGenes$ProcessThread.class
 %%JAVAJARDIR%%/bbmap/prok/CallGenes.class
 %%JAVAJARDIR%%/bbmap/prok/CallGenes.java
-%%JAVAJARDIR%%/bbmap/prok/Feature$FeatureComparatorScore.class
-%%JAVAJARDIR%%/bbmap/prok/Feature.class
-%%JAVAJARDIR%%/bbmap/prok/Feature.java
 %%JAVAJARDIR%%/bbmap/prok/FetchProks$ProcessThread.class
 %%JAVAJARDIR%%/bbmap/prok/FetchProks$Stats.class
 %%JAVAJARDIR%%/bbmap/prok/FetchProks.class
@@ -1367,6 +1630,9 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/prok/MergeRibo_Fast.java
 %%JAVAJARDIR%%/bbmap/prok/Orf.class
 %%JAVAJARDIR%%/bbmap/prok/Orf.java
+%%JAVAJARDIR%%/bbmap/prok/PFeature$FeatureComparatorScore.class
+%%JAVAJARDIR%%/bbmap/prok/PFeature.class
+%%JAVAJARDIR%%/bbmap/prok/PFeature.java
 %%JAVAJARDIR%%/bbmap/prok/PGMTools$1.class
 %%JAVAJARDIR%%/bbmap/prok/PGMTools.class
 %%JAVAJARDIR%%/bbmap/prok/PGMTools.java
@@ -1384,8 +1650,22 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/prok/SplitRibo.java
 %%JAVAJARDIR%%/bbmap/prok/StatsContainer.class
 %%JAVAJARDIR%%/bbmap/prok/StatsContainer.java
+%%JAVAJARDIR%%/bbmap/repeat/Palindrome.class
+%%JAVAJARDIR%%/bbmap/repeat/Palindrome.java
+%%JAVAJARDIR%%/bbmap/repeat/PalindromeFinder.class
+%%JAVAJARDIR%%/bbmap/repeat/PalindromeFinder.java
+%%JAVAJARDIR%%/bbmap/repeat/Repeat$PosComparator.class
+%%JAVAJARDIR%%/bbmap/repeat/Repeat$PosComparator2.class
+%%JAVAJARDIR%%/bbmap/repeat/Repeat.class
+%%JAVAJARDIR%%/bbmap/repeat/Repeat.java
+%%JAVAJARDIR%%/bbmap/repeat/RepeatFinder$ProcessThread.class
+%%JAVAJARDIR%%/bbmap/repeat/RepeatFinder.class
+%%JAVAJARDIR%%/bbmap/repeat/RepeatFinder.java
+%%JAVAJARDIR%%/bbmap/repeat/RepeatSet.class
+%%JAVAJARDIR%%/bbmap/repeat/RepeatSet.java
 %%JAVAJARDIR%%/bbmap/server/PercentEncoding.class
 %%JAVAJARDIR%%/bbmap/server/PercentEncoding.java
+%%JAVAJARDIR%%/bbmap/server/ServerTools$1.class
 %%JAVAJARDIR%%/bbmap/server/ServerTools.class
 %%JAVAJARDIR%%/bbmap/server/ServerTools.java
 %%JAVAJARDIR%%/bbmap/server/SimpleHttpServer$GetHandler.class
@@ -1395,6 +1675,28 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/shared/Colors.java
 %%JAVAJARDIR%%/bbmap/shared/KillSwitch.class
 %%JAVAJARDIR%%/bbmap/shared/KillSwitch.java
+%%JAVAJARDIR%%/bbmap/shared/LineParser.class
+%%JAVAJARDIR%%/bbmap/shared/LineParser.java
+%%JAVAJARDIR%%/bbmap/shared/LineParser1.class
+%%JAVAJARDIR%%/bbmap/shared/LineParser1.java
+%%JAVAJARDIR%%/bbmap/shared/LineParser2.class
+%%JAVAJARDIR%%/bbmap/shared/LineParser2.java
+%%JAVAJARDIR%%/bbmap/shared/LineParser4.class
+%%JAVAJARDIR%%/bbmap/shared/LineParser4.java
+%%JAVAJARDIR%%/bbmap/shared/LineParserS.class
+%%JAVAJARDIR%%/bbmap/shared/LineParserS.java
+%%JAVAJARDIR%%/bbmap/shared/LineParserS1.class
+%%JAVAJARDIR%%/bbmap/shared/LineParserS1.java
+%%JAVAJARDIR%%/bbmap/shared/LineParserS2.class
+%%JAVAJARDIR%%/bbmap/shared/LineParserS2.java
+%%JAVAJARDIR%%/bbmap/shared/LineParserS3.class
+%%JAVAJARDIR%%/bbmap/shared/LineParserS3.java
+%%JAVAJARDIR%%/bbmap/shared/LineParserS4.class
+%%JAVAJARDIR%%/bbmap/shared/LineParserS4.java
+%%JAVAJARDIR%%/bbmap/shared/LineParserS4Reverse.class
+%%JAVAJARDIR%%/bbmap/shared/LineParserS4Reverse.java
+%%JAVAJARDIR%%/bbmap/shared/LineParserSimple.class
+%%JAVAJARDIR%%/bbmap/shared/LineParserSimple.java
 %%JAVAJARDIR%%/bbmap/shared/MetadataWriter.class
 %%JAVAJARDIR%%/bbmap/shared/MetadataWriter.java
 %%JAVAJARDIR%%/bbmap/shared/Parse.class
@@ -1405,16 +1707,19 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/shared/PreParser.java
 %%JAVAJARDIR%%/bbmap/shared/Primes.class
 %%JAVAJARDIR%%/bbmap/shared/Primes.java
-%%JAVAJARDIR%%/bbmap/shared/ReadStats.class
-%%JAVAJARDIR%%/bbmap/shared/ReadStats.java
+%%JAVAJARDIR%%/bbmap/shared/SIMD.class
+%%JAVAJARDIR%%/bbmap/shared/SIMD.java
 %%JAVAJARDIR%%/bbmap/shared/Shared.class
 %%JAVAJARDIR%%/bbmap/shared/Shared.java
 %%JAVAJARDIR%%/bbmap/shared/Timer.class
 %%JAVAJARDIR%%/bbmap/shared/Timer.java
+%%JAVAJARDIR%%/bbmap/shared/Tools$1.class
 %%JAVAJARDIR%%/bbmap/shared/Tools.class
 %%JAVAJARDIR%%/bbmap/shared/Tools.java
 %%JAVAJARDIR%%/bbmap/shared/TrimRead.class
 %%JAVAJARDIR%%/bbmap/shared/TrimRead.java
+%%JAVAJARDIR%%/bbmap/shared/Vector.class
+%%JAVAJARDIR%%/bbmap/shared/Vector.java
 %%JAVAJARDIR%%/bbmap/sketch/AddSSU$SketchHeader.class
 %%JAVAJARDIR%%/bbmap/sketch/AddSSU.class
 %%JAVAJARDIR%%/bbmap/sketch/AddSSU.java
@@ -1518,6 +1823,10 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/sort/MergeSorted.java
 %%JAVAJARDIR%%/bbmap/sort/ReadComparator.class
 %%JAVAJARDIR%%/bbmap/sort/ReadComparator.java
+%%JAVAJARDIR%%/bbmap/sort/ReadComparatorClump.class
+%%JAVAJARDIR%%/bbmap/sort/ReadComparatorClump.java
+%%JAVAJARDIR%%/bbmap/sort/ReadComparatorCrispr.class
+%%JAVAJARDIR%%/bbmap/sort/ReadComparatorCrispr.java
 %%JAVAJARDIR%%/bbmap/sort/ReadComparatorFlowcell.class
 %%JAVAJARDIR%%/bbmap/sort/ReadComparatorFlowcell.java
 %%JAVAJARDIR%%/bbmap/sort/ReadComparatorID.class
@@ -1536,6 +1845,8 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/sort/ReadComparatorTaxa.java
 %%JAVAJARDIR%%/bbmap/sort/ReadComparatorTopological.class
 %%JAVAJARDIR%%/bbmap/sort/ReadComparatorTopological.java
+%%JAVAJARDIR%%/bbmap/sort/ReadComparatorTopological5Bit.class
+%%JAVAJARDIR%%/bbmap/sort/ReadComparatorTopological5Bit.java
 %%JAVAJARDIR%%/bbmap/sort/ReadErrorComparator.class
 %%JAVAJARDIR%%/bbmap/sort/ReadErrorComparator.java
 %%JAVAJARDIR%%/bbmap/sort/ReadLengthComparator.class
@@ -1555,12 +1866,6 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/sort/SortReadsByID$Block.class
 %%JAVAJARDIR%%/bbmap/sort/SortReadsByID.class
 %%JAVAJARDIR%%/bbmap/sort/SortReadsByID.java
-%%JAVAJARDIR%%/bbmap/star/Ship.class
-%%JAVAJARDIR%%/bbmap/star/Ship.java
-%%JAVAJARDIR%%/bbmap/star/Simulate.class
-%%JAVAJARDIR%%/bbmap/star/Simulate.java
-%%JAVAJARDIR%%/bbmap/star/Weapon.class
-%%JAVAJARDIR%%/bbmap/star/Weapon.java
 %%JAVAJARDIR%%/bbmap/stream/ArrayListSet$Pack.class
 %%JAVAJARDIR%%/bbmap/stream/ArrayListSet.class
 %%JAVAJARDIR%%/bbmap/stream/ArrayListSet.java
@@ -1595,6 +1900,8 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/stream/CrisContainer.java
 %%JAVAJARDIR%%/bbmap/stream/CrisWrapper.class
 %%JAVAJARDIR%%/bbmap/stream/CrisWrapper.java
+%%JAVAJARDIR%%/bbmap/stream/CustomHeader.class
+%%JAVAJARDIR%%/bbmap/stream/CustomHeader.java
 %%JAVAJARDIR%%/bbmap/stream/DualCris.class
 %%JAVAJARDIR%%/bbmap/stream/DualCris.java
 %%JAVAJARDIR%%/bbmap/stream/EmblReadInputStream.class
@@ -1611,8 +1918,6 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/stream/FastqReadInputStream.java
 %%JAVAJARDIR%%/bbmap/stream/GbkReadInputStream.class
 %%JAVAJARDIR%%/bbmap/stream/GbkReadInputStream.java
-%%JAVAJARDIR%%/bbmap/stream/Header.class
-%%JAVAJARDIR%%/bbmap/stream/Header.java
 %%JAVAJARDIR%%/bbmap/stream/HeaderInputStream.class
 %%JAVAJARDIR%%/bbmap/stream/HeaderInputStream.java
 %%JAVAJARDIR%%/bbmap/stream/MDWalker.class
@@ -1625,6 +1930,18 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/stream/MultiCros3$Buffer.class
 %%JAVAJARDIR%%/bbmap/stream/MultiCros3.class
 %%JAVAJARDIR%%/bbmap/stream/MultiCros3.java
+%%JAVAJARDIR%%/bbmap/stream/MultiCros4$Buffer.class
+%%JAVAJARDIR%%/bbmap/stream/MultiCros4$RetireThread.class
+%%JAVAJARDIR%%/bbmap/stream/MultiCros4$Token.class
+%%JAVAJARDIR%%/bbmap/stream/MultiCros4.class
+%%JAVAJARDIR%%/bbmap/stream/MultiCros4.java
+%%JAVAJARDIR%%/bbmap/stream/MultiCros5$Buffer.class
+%%JAVAJARDIR%%/bbmap/stream/MultiCros5.class
+%%JAVAJARDIR%%/bbmap/stream/MultiCros5.java
+%%JAVAJARDIR%%/bbmap/stream/MultiCros6$Buffer.class
+%%JAVAJARDIR%%/bbmap/stream/MultiCros6$TimestampComparator.class
+%%JAVAJARDIR%%/bbmap/stream/MultiCros6.class
+%%JAVAJARDIR%%/bbmap/stream/MultiCros6.java
 %%JAVAJARDIR%%/bbmap/stream/NullOutputStream.class
 %%JAVAJARDIR%%/bbmap/stream/NullOutputStream.java
 %%JAVAJARDIR%%/bbmap/stream/OnelineReadInputStream.class
@@ -1680,24 +1997,36 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/structures/AbstractIntHashMap.java
 %%JAVAJARDIR%%/bbmap/structures/AtomicBitSet.class
 %%JAVAJARDIR%%/bbmap/structures/AtomicBitSet.java
+%%JAVAJARDIR%%/bbmap/structures/AtomicStringNum.class
+%%JAVAJARDIR%%/bbmap/structures/AtomicStringNum.java
 %%JAVAJARDIR%%/bbmap/structures/ByteBuilder.class
 %%JAVAJARDIR%%/bbmap/structures/ByteBuilder.java
+%%JAVAJARDIR%%/bbmap/structures/CRange.class
+%%JAVAJARDIR%%/bbmap/structures/CRange.java
 %%JAVAJARDIR%%/bbmap/structures/CoverageArray.class
 %%JAVAJARDIR%%/bbmap/structures/CoverageArray.java
 %%JAVAJARDIR%%/bbmap/structures/CoverageArray2.class
 %%JAVAJARDIR%%/bbmap/structures/CoverageArray2.java
+%%JAVAJARDIR%%/bbmap/structures/CoverageArray2A.class
+%%JAVAJARDIR%%/bbmap/structures/CoverageArray2A.java
 %%JAVAJARDIR%%/bbmap/structures/CoverageArray3.class
 %%JAVAJARDIR%%/bbmap/structures/CoverageArray3.java
 %%JAVAJARDIR%%/bbmap/structures/CoverageArray3A.class
 %%JAVAJARDIR%%/bbmap/structures/CoverageArray3A.java
+%%JAVAJARDIR%%/bbmap/structures/Crispr.class
+%%JAVAJARDIR%%/bbmap/structures/Crispr.java
 %%JAVAJARDIR%%/bbmap/structures/DoubleList.class
 %%JAVAJARDIR%%/bbmap/structures/DoubleList.java
-%%JAVAJARDIR%%/bbmap/structures/EntropyTracker.class
-%%JAVAJARDIR%%/bbmap/structures/EntropyTracker.java
+%%JAVAJARDIR%%/bbmap/structures/Feature.class
+%%JAVAJARDIR%%/bbmap/structures/Feature.java
 %%JAVAJARDIR%%/bbmap/structures/FloatList.class
 %%JAVAJARDIR%%/bbmap/structures/FloatList.java
+%%JAVAJARDIR%%/bbmap/structures/Heap$HeapIterator.class
 %%JAVAJARDIR%%/bbmap/structures/Heap.class
 %%JAVAJARDIR%%/bbmap/structures/Heap.java
+%%JAVAJARDIR%%/bbmap/structures/HeapLoc$HeapIterator.class
+%%JAVAJARDIR%%/bbmap/structures/HeapLoc.class
+%%JAVAJARDIR%%/bbmap/structures/HeapLoc.java
 %%JAVAJARDIR%%/bbmap/structures/IntHashMap.class
 %%JAVAJARDIR%%/bbmap/structures/IntHashMap.java
 %%JAVAJARDIR%%/bbmap/structures/IntHashMapBinary.class
@@ -1720,6 +2049,8 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/structures/IntMap.java
 %%JAVAJARDIR%%/bbmap/structures/ListNum.class
 %%JAVAJARDIR%%/bbmap/structures/ListNum.java
+%%JAVAJARDIR%%/bbmap/structures/LongArrayListHashMap.class
+%%JAVAJARDIR%%/bbmap/structures/LongArrayListHashMap.java
 %%JAVAJARDIR%%/bbmap/structures/LongHashMap.class
 %%JAVAJARDIR%%/bbmap/structures/LongHashMap.java
 %%JAVAJARDIR%%/bbmap/structures/LongHashSet.class
@@ -1743,20 +2074,44 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/structures/LongListSet.java
 %%JAVAJARDIR%%/bbmap/structures/LongLongHashMap.class
 %%JAVAJARDIR%%/bbmap/structures/LongLongHashMap.java
+%%JAVAJARDIR%%/bbmap/structures/LongLongHashMapHybrid.class
+%%JAVAJARDIR%%/bbmap/structures/LongLongHashMapHybrid.java
+%%JAVAJARDIR%%/bbmap/structures/LongLongListHashMap.class
+%%JAVAJARDIR%%/bbmap/structures/LongLongListHashMap.java
 %%JAVAJARDIR%%/bbmap/structures/LongM.class
 %%JAVAJARDIR%%/bbmap/structures/LongM.java
 %%JAVAJARDIR%%/bbmap/structures/LongPair.class
 %%JAVAJARDIR%%/bbmap/structures/LongPair.java
 %%JAVAJARDIR%%/bbmap/structures/MultiBitSet.class
 %%JAVAJARDIR%%/bbmap/structures/MultiBitSet.java
-%%JAVAJARDIR%%/bbmap/structures/PolymerTracker.class
-%%JAVAJARDIR%%/bbmap/structures/PolymerTracker.java
+%%JAVAJARDIR%%/bbmap/structures/Point.class
+%%JAVAJARDIR%%/bbmap/structures/Point.java
 %%JAVAJARDIR%%/bbmap/structures/Quantizer.class
 %%JAVAJARDIR%%/bbmap/structures/Quantizer.java
 %%JAVAJARDIR%%/bbmap/structures/Range.class
 %%JAVAJARDIR%%/bbmap/structures/Range.java
 %%JAVAJARDIR%%/bbmap/structures/RawBitSet.class
 %%JAVAJARDIR%%/bbmap/structures/RawBitSet.java
+%%JAVAJARDIR%%/bbmap/structures/SeqCount.class
+%%JAVAJARDIR%%/bbmap/structures/SeqCount.java
+%%JAVAJARDIR%%/bbmap/structures/SeqCountM.class
+%%JAVAJARDIR%%/bbmap/structures/SeqCountM.java
+%%JAVAJARDIR%%/bbmap/structures/SeqMap$1.class
+%%JAVAJARDIR%%/bbmap/structures/SeqMap$2.class
+%%JAVAJARDIR%%/bbmap/structures/SeqMap$3.class
+%%JAVAJARDIR%%/bbmap/structures/SeqMap.class
+%%JAVAJARDIR%%/bbmap/structures/SeqMap.java
+%%JAVAJARDIR%%/bbmap/structures/SeqPos.class
+%%JAVAJARDIR%%/bbmap/structures/SeqPos.java
+%%JAVAJARDIR%%/bbmap/structures/SeqPosM.class
+%%JAVAJARDIR%%/bbmap/structures/SeqPosM.java
+%%JAVAJARDIR%%/bbmap/structures/SetLoc.class
+%%JAVAJARDIR%%/bbmap/structures/SetLoc.java
+%%JAVAJARDIR%%/bbmap/structures/StandardDeviator$ProcessThread.class
+%%JAVAJARDIR%%/bbmap/structures/StandardDeviator.class
+%%JAVAJARDIR%%/bbmap/structures/StandardDeviator.java
+%%JAVAJARDIR%%/bbmap/structures/StringCount.class
+%%JAVAJARDIR%%/bbmap/structures/StringCount.java
 %%JAVAJARDIR%%/bbmap/structures/StringNum.class
 %%JAVAJARDIR%%/bbmap/structures/StringNum.java
 %%JAVAJARDIR%%/bbmap/structures/StringPair.class
@@ -1782,6 +2137,8 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/tax/FindAncestor.java
 %%JAVAJARDIR%%/bbmap/tax/GiToTaxid.class
 %%JAVAJARDIR%%/bbmap/tax/GiToTaxid.java
+%%JAVAJARDIR%%/bbmap/tax/GiToTaxidInt.class
+%%JAVAJARDIR%%/bbmap/tax/GiToTaxidInt.java
 %%JAVAJARDIR%%/bbmap/tax/IDNode.class
 %%JAVAJARDIR%%/bbmap/tax/IDNode.java
 %%JAVAJARDIR%%/bbmap/tax/IDTree.class
@@ -1837,11 +2194,16 @@ libexec/bbmap/webcheck.sh
 %%JAVAJARDIR%%/bbmap/template/A_SampleBasic2.java
 %%JAVAJARDIR%%/bbmap/template/A_SampleByteFile.class
 %%JAVAJARDIR%%/bbmap/template/A_SampleByteFile.java
+%%JAVAJARDIR%%/bbmap/template/A_SampleByteFileMT$ProcessThread.class
+%%JAVAJARDIR%%/bbmap/template/A_SampleByteFileMT.class
+%%JAVAJARDIR%%/bbmap/template/A_SampleByteFileMT.java
 %%JAVAJARDIR%%/bbmap/template/A_SampleD.class
 %%JAVAJARDIR%%/bbmap/template/A_SampleD.java
 %%JAVAJARDIR%%/bbmap/template/A_SampleMT$ProcessThread.class
 %%JAVAJARDIR%%/bbmap/template/A_SampleMT.class
 %%JAVAJARDIR%%/bbmap/template/A_SampleMT.java
*** 29 LINES SKIPPED ***