Version 0.3.6

This update contains mostly reliability improvements.

Important: Besides that, it implements a new compression for the index of suffix ranges. The de Bruijn graphs constructed with older versions of MetaGraph have to be reindexed with metagraph transform -o graph_updated graph.dbg -v -p <NUM_THREADS>

What's Changed

• detect max number of open files and limit num chunks merged by @karasikov in #411
• Server now reports the max score for a query sequence by @hmusta in #414
• Use 1 file per EliasFano stream for faster construction with fewer open files by @karasikov in #415
• retry on failed write in sdsl::int_vector_buffer by @karasikov in #422
• Retry on failed read by @karasikov in #429
• Discard edges to dummy nodes in GFA assembly by @hmusta in #428
• Workaround for bug in g++-8.2 by @hmusta in #425
• Compress node ranges index (=> index longer suffixes with less memory overhead) by @karasikov in #417
• Various improvements and fixes in annotations by @karasikov in #423

Full Changelog: v0.3.5...v0.3.6

Version 0.3.5

What's Changed

• Alignment to labeled subgraphs and counting DBGs
• Other improvements and fixes in alignment algorithms (chaining, seeding, etc.)
• Reduce memory usage in seed generation, seed extension improvements
• allow renaming labels in arbitrary annotations
• support annotating coordinates with disk swap
• improved usage help description for flags
• updated external libraries to support compiling with AppleClang 13.1.6

Full Changelog: v0.3.4...v0.3.5

Version 0.3.4

What's Changed

• Query expressions (counts) in labels for individual k-mers in query
• Updated the MetaGraph API package
• more docs
• Support printing version of the binary
• Also pre-compile binaries without AVX2 and MSSE4.2

Full Changelog: v0.3.3...v0.3.4

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The pre-compiled binaries (only for Linux) are statically linked and hence don't require additional libraries to be installed.
The *_noAVX binaries are compiled without the modern AVX2 and MSSE4.2 instructions and should be used on older processors in case normal binaries cannot be run.

Version 0.3.3

What's Changed

• API support for count/coord indexes, parallel search in multiple indexes
• hide some rarely used flags from default help messages in CLI
• output counts for aggregated columns
• refactoring and cleanups in row diff annotations
• fixed default user permissions in docker containers (now does not require changing permissions or resetting the user)
• more docs

New Contributors

• @thomastzhou made their first contribution in #358

Full Changelog: v0.3.2...v0.3.3

Version 0.3.2

What's Changed

• Differential assembly refactoring
• Support differential assembly on canonical and primary graphs
• Column aggregation with k-mer filtering based on counts (currently only for ColumnCompressed formats)
• In-place graph initialization and serialization for lower memory usage
• Graph construction reliability improvements
• Other fixes and cleanups
• Updates in docs

Full Changelog: v0.3.1...v0.3.2

Version 0.3.1

• Fixed alignment behavior with flag --fwd-and-reverse (align both strands independently and report their results separately)

Version 0.3.0

Major updates since v0.2.0

• Count annotations: represent k-mer counts, encode abundances or gene expression

  • query count annotation in #309
  • delta-coding of k-mer count annotations in #315
  • query k-mer count quantiles in #331

• Coordinate annotations: represent k-mer coordinates (all occurrences in the source) in multi-integer annotations (=> lossless indexing of sequences, encoding of sequence traces)

  • index and query k-mer coordinates in #326, #337, #338, #341, #345
  • coordinate annotations with Multi-BRWT base in #353

Other new features:

• window smoothing of k-mer counts within unitigs in #316
• print histogram of k-mer weights (counts) in #351
• new query parameter: filter results by the number of k-mers matched to the joint graph in #339
• skeleton for taxonomic classification in #343 and #346

Enhancements:

• Alignment refactor and rewrite in #333
• Chain local alignments to improve accuracy of long read alignment in #335
• optimized storage of labels in batch annotator (=> faster queries, reduced RAM) in #350
• improvements in column aggregation in #314
• support row-diff transform in memory without disk swap in #342
• parallel transforms for changing graph state (e.g., small->stat) in #312
• serialize node weights immediately when building graph (=> reduced RAM) in #317
• improved parallelization of annotating sequence batches in #322
• bit_vector_sd::conditional_rank1 for faster DBGBitmap::map_to_nodes in #323
• various other tweaks and cleanups
• sphinx documentation

Deployment:

• docker containers are now published on ghcr.io (see https://github.com/ratschlab/metagraph/pkgs/container/metagraph)

Full Changelog: v0.2.0...v0.3.0

Version 0.2.0

• Streamlined and simplified annotation conversions
  • simplifications and improvements in CLI
  • always save linkage matrix generated for Multi-BRWT
• RowDiff 2.0
  • better anchor assignment (nodes with negative size reduction are anchored first, then additional anchors are assigned to satisfy the constraints)
  • support optimized routing at forks
  • changed the construction flow and improved CLI
• Adaptive subsampling with 64-bit indexes for managing larger ranges in very sparse columns
• Support for column intersection (build a new column as AND/OR/%-threshold from input columns)
• Other fixes and optimizations

First release on conda and docker

Feature/cleanup dockerfiles (#299)

* creating multi stage dockerfile, adjusting Makefile accordingly

* properly including ccache also in docker containers

* updating top level README with docker related things