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CHANGELOG.md

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pbcopper - CHANGELOG

Active

Fixed

  • Data::Read::ClipTo on quality values

[2.2.0] - 2022-01-03

Added

  • Allow description array in positional args

Changed

  • Cleaned up CLI parsing error messages
  • Fixed FireAndForget exception handling
  • Fixed alarm API for empty file
  • Update nlohmann/json to 3.11.2

[2.1.0] - 2022-07-26

Added

  • ValidateCigar
  • LeftAlignCigar
  • UnorderedMap, UnorderedSet
  • KMerIndex, LSHIndex, FastMod
  • Concurrent queues (SPSC, MPMC) from rigtorp

Changed

  • Updated robin_hood to v3.11.5

[2.0.0] - 2022-01-10

Changed

  • C++20 is now a hard minimum.

[1.9.5] - 2021-12-07

Added

  • Heteroduplex finder algorithm
  • Fisher's exact test

[1.9.4] - 2021-12-06

Added

  • "--all-help" and "--show-all-help" to CLI, to include hidden options in help output

Changed

  • Update JSON impl to 3.10.4

[1.9.3] - 2021-09-21

Fixed

  • Catch out of bounds in Sparc

[1.9.2] - 2021-07-01

Added

  • Add Sparc implementation from unanimity
  • Add TimeReporter for conditionally logging timing info
  • Add "research use only" disclaimer to help display
  • Add context message for missing positional arg in CLI
  • Add scientific notation support in CLI
  • Add confusion matrix helper

[1.9.1] - 2021-02-16

Added

  • Utility::Shuffle for portable alternative to std::shuffle
  • Parallel::Dispatch to submit jobs to an existing FireAndForget

Changed

  • Read.h pulse width is now optional to allow kinetic-free subreads as input

[1.9.0] - 2020-12-22

Added

  • Interval tree from unanimity
  • Sparse POA implementation, outsourced from unanimity
  • edlib wrapper API
  • "Normalized" thread count utility
  • Add KSW2
  • Support ARM compile target
  • Add SIMDE to third-party sources

[1.8.0] - 2020-09-23

Added

  • Base64 encoding/decoding
  • (Simplified) alarm file can be created for general exceptions
  • Utility::StringView as std::string_view look-a-like
  • Support for hidden CLI subtools
  • Support for alternate frame codecs

Changed

  • Accuracy explicitly allows -1, otherwise clamps to [0.0, 1.0]
  • Fixed FaF and FaFI exception handling

[1.7.0] - 2020-05-22

Added

  • PartitionElements utility
  • Version printing callbacks for CLI
  • Ssize utility
  • Knock-first graph
  • VERBOSE log level
  • Dagcon API
  • LibraryInfo API

Changed

  • Now using (signed) Data::Position in Data::Read.
  • Data::SNR values changed from double to float.

Fixed

  • ReadId from CCS read names
  • More robust random number generators (for UUIDs).
    • getrandom() requires Linux kernel 3.17+
    • getentropy() requires glibc 2.25+

Removed

  • Unused SystemInfo utility

[1.6.0] - 2020-04-10

Removed

  • CLI version 1 (pbcopper/cli/*)

[1.5.0] - 2020-03-12

Added

  • pbmer API - DeBruijn graph & kmers
  • AlarmException for generating JSON alarms
  • Allow SI suffixes in command line arguments
  • std::ostream redirection utilities

Changed

  • Double-precision in Stopwatch

Fixed

  • WorkQueue deadlock if exception was thrown in consumer task

Removed

  • InstallSignalHandlers() from logging

[1.4.0] - 2019-11-05

Added

  • Consolidated & cleanup of core data structures shared between pbcopper/unanimity/pbbam
  • CLI_v2 now maintains logger setup & lifetime
  • Alarms API

[1.3.0] - 2019-06-11

Added

  • Alignment algorithms from unanimity (local alignment, semi-global, affine, etc)

Removed

  • Unused CallbackTimer
  • Unused PacBio::Stream utilities

[1.2.0] - 2019-05-03

Changed

  • CLI_v2::Results::NumProcessors() changed to CLI_v2::Results::NumThreads() for clarity.

Added

  • Convenience methods for CLI_v2 clients: default log level override, explicit access to built-ins, built-in 'num-threads' option.

[1.1.0] - 2019-04-29

Added

  • Reports module

[1.0.0] - 2019-04-23

Changed

  • C++14 is now a hard minimum.

Removed

  • Headers emulating C++14 features for C++11.

Added

  • New (opt-in) CLI version 2.

[0.5.0] - 2019-04-11

Changed

  • Requires C++14 at minimum.

[0.3.0] - 2018-04-30

Changed

  • Minor ToolContract::Config API change.

[0.2.0] - 2017-12-03

Added

  • WorkQueue for parallel execution

[0.1.1] - 2017-09-26

Changed

  • UNUSED macro to no-op method

[0.1.0] - 2017-01-13

Added

  • Encapsulate project version and git sha1
  • RSMovieName & RSReadName: Sequel and RSII movie names are composed of different data, and thus need to be handled separately. MovieName & ReadName handle Sequel-style data as the default.
  • GoogleTest/GoogleMock in third-party/googletest
  • Access to input command line from PacBio::CLI::Results
  • QGramIndex & seed results
  • Added support for new tool contract data model: option choices & modified JSON format.
  • Added basic option groups to CLI::Interface.

[0.0.1] - 2016-06-22

Added

  • PacBio::CLI : command-line parsing & tool-contract integration
    • CLI - entry-point methods for parsing args & invoking application callback
    • Interface - define application's options, description, etc.
    • Results - contains the results of arg parsing (or resolved tool contract), will be passed to the application callback
    • ToolContract sub-namespace: contains all APIs for setting up tool contract integration
  • PacBio::Data: main data types & data structures
    • Interval, Position, Zmw - basic data types (same as pbbam)
    • MovieName - query parts of a PacBio movie name
    • ReadName - query parts of a PacBio read name
  • PacBio::JSON : JSON support
    • Json - wrapper around nlohmann::json
  • PacBio::Logging : logging utilities
    • Logger, LogMessage, etc - basic logging (same as pbccs)
  • PacBio::Stream : functional-programming-like data streaming
    • data Source, Sink, & Transform typedefs
    • instantiated with client-defined 'callables' (lambdas, free functions, static public member functions)
    • connected via operator >>
  • PacBio::Utility : miscellaneous utilities
    • CallbackTimer - schedule periodic callback invokation (or delayed single-shot)
    • EnumClassHash - allows enums/enum classes to be used as STL hash keys
    • Stopwatch - timer for benchmarking, logging, etc
    • StringUtils - string dicing & splicing utilities
    • SystemInfo - currently provides endianness
  • Examples
    • cli_demo - playground for testing the command line interface
  • Tests
    • Unit tests for all classes/modules added