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Commits on Aug 4, 2024

• [doc] fix documentation for --input-alphabet

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• [misc] update citation and copyright

  h-2

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• [misc] bump version

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Commits on Jan 9, 2024

• [fix] check presence of taxtree in index

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Commits on Dec 19, 2023

• Fix zlib support for static macos build

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Commits on Dec 14, 2023

• Allow .fna and .faa fasta extensions

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Commits on Nov 26, 2023

• [feature] add pairs profiles

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• [fix] exception handling of the sharg-parser

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• [fix] pairs counting

  h-2

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• [misc] redesign widening, merging and prefilter of matches; change band to sqrt

  h-2

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Commits on Nov 17, 2023

• [fix] alignment bug

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Commits on Jul 25, 2023

• [misc] remove dispatcher; clean-up cmake

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Commits on Jul 21, 2023

• [misc] track biocpp changes and gcc13

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Commits on Jul 17, 2023

• [fix] static builds

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Commits on Jul 12, 2023

• [misc] deactivate BIFM by default

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• Switch to max evalue

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Commits on May 9, 2023

• Merge pull request #210 from h-2/size_sum

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Commits on May 3, 2023

• Update src/mkindex_algo.hpp

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• fix: update to newest fmindex_collection

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• [misc] db size

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Commits on Apr 27, 2023

• Add parameters for bisulfite profiles

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Commits on Apr 15, 2023

• [misc] resolve many TODOs, get rid of regex parsing

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Commits on Apr 3, 2023

• [feature] query preloading

  h-2

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Commits on Mar 21, 2023

• add searchbs and mkindexbs as proper commands

  h-2

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Commits on Feb 14, 2023

• [misc] allow dna15 in subject sequences

  h-2

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Commits on Jan 9, 2023

• [feature] compressed indexes

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Commits on Dec 6, 2022

• [misc] potential optimisations

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• [misc] apply review comments and some cleanup

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Commits on Nov 30, 2022

• [fix] build with GCC10's libstdc++

  h-2

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• [infra] add cereal (prvsly included in seqan3)

  h-2

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• cleanup of last seqan3 bits

  h-2

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• replace crufty manual io with biocpp-io

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• pull async_input_buffer into lambda + minor stuff

  h-2

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• replace seqan3 prescoring with seqan2

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Commits on Nov 29, 2022

• seqan3 → biocpp step1

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