[med-svn] [Git][med-team/bbmap][upstream] New upstream version 39.20+dfsg

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch upstream at Debian Med / bbmap


Commits:
6ae3d455 by Étienne Mollier at 2025-04-05T13:50:21+02:00
New upstream version 39.20+dfsg
- - - - -


59 changed files:

- README.md
- checkstrand.sh
- current/aligner/MicroAligner3.java
- + current/aligner/MicroWrapper.java
- current/aligner/SideChannel3.java
- current/barcode/CountBarcodes2.java
- current/barcode/PCRMatrix.java
- current/bin/AllToAllVectorMaker.java
- current/bin/Bin.java
- current/bin/BinObject.java
- current/bin/BinStats.java
- current/bin/Binner.java
- current/bin/Cluster.java
- current/bin/Contig.java
- current/bin/ContigRenamer.java
- current/bin/DataLoader.java
- current/bin/GradeBins.java
- current/bin/Key.java
- + current/bin/KmerProb.java
- current/bin/Oracle.java
- current/bin/QuickBin.java
- current/bin/RandomReadsMG.java
- current/bin/SamLoader.java
- current/bin/SimilarityMeasures.java
- current/bin/SpectraCounter.java
- current/fileIO/FileFormat.java
- current/hiseq/PlotFlowCell.java
- current/jgi/BBDuk.java
- current/jgi/BBMerge.java
- current/jgi/CheckStrand.java
- current/jgi/CheckStrand2.java
- current/jgi/RQCFilter2.java
- current/jgi/Shred.java
- current/ml/CellNet.java
- current/ml/DataLoader.java
- current/ml/Trainer.java
- current/prok/Orf.java
- current/shared/Shared.java
- current/shared/Tools.java
- current/stream/SamLine.java
- current/structures/FloatList.java
- current/structures/LongPair.java
- current/structures/Range.java
- gradebins.sh
- makequickbinvector.sh
- + microalign.sh
- quickbin.sh
- randomreadsmg.sh
- + resources/phix_adapters.fa
- + resources/polya.fa
- + resources/polyc.fa
- + resources/polyg.fa
- + resources/polyt.fa
- + resources/quickbin1D.bbnet
- + resources/quickbin1D_all.bbnet
- + resources/quickbinND.bbnet
- + resources/quickbinND_all.bbnet
- + resources/shred4merFractions.tsv
- shred.sh


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/bbmap/-/commit/6ae3d455a5b891aad671a02f740dac71c8799a1d

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View it on GitLab: https://salsa.debian.org/med-team/bbmap/-/commit/6ae3d455a5b891aad671a02f740dac71c8799a1d
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