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CHANGELOG.md

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Changelog

Unreleased

Changed

  • Log messages are written to stderr rather than stdout.

Removed

  • Remove --verbose flag.

    Logging is always enabled. This flag was previously deprecated in 0.8.0.

0.12.0 - 2024-07-08

Added

  • commands/lint: Add --record-definition-separator option (#34).

    This allows a custom separator to be used to strip the description from a record name. When unset, the default remains the same with '/' and ' '.

0.11.0 - 2023-09-07

Changed

  • commands/lint: Return a nonzero exit code if an error is logged.

    When the lint mode is set to log, the lint command will now exit with a nonzero status if there are any validation errors.

0.10.0 - 2023-04-04

Added

  • commands/filter: Add filter by sequence pattern (#27).

    Records can be filtered by their sequence using a regular expression: fq filter --sequence-pattern <regex> --dsts <dst> <src>. It cannot be combined with name filtering.

Changed

  • commands/filter: Support multiple segments (#30).

    The filter command now supports multiple segments. Each source is paired with a destination (i.e., the output is no longer written to stdout by default), which is filtered by whether the record in the first segment is matched.

  • commands/subsample: Disallow 0% and 100% as probabilities.

    At these extremes, use touch and cp, respectively, instead.

0.9.1 - 2022-02-15

Fixed

  • commands/subsample: Count the lines from the decompressed data if the input is gzipped.

    Used in the exact sampler, this previously counted "lines" from the compressed input.

  • commands/subsample: Clamp the destination record count to the range of the source record count.

    Otherwise, this would cause the filter to never finish building.

0.9.0 - 2022-02-10

Added

  • commands/subsample: Add exact sampler.

    This writes an exact number of samples to the output. Set the -n/--record-count option to use the exact sampler.

Changed

  • Update argument parser to clap 3.

0.8.0 - 2021-11-12

Changed

  • Rename project to fq.

Added

  • commands/generate: Add -s short option for --seed.

  • commands: Add subsample command.

    subsample outputs a proportional subset of records from single or paired FASTQ files.

Deprecated

  • Deprecate --verbose flag.

    Logging is now always enabled.

0.7.1 - 2021-10-07

Fixed

  • main: Show global version in subcommands (#20).

    This allows subcommands to show the global version, e.g., fq lint --version.

0.7.0 - 2021-05-07

Added

  • generate: Added --read-length option to set the number of bases to generate in each record's sequence.

0.6.0 - 2020-12-17

Added

  • The FASTQ reader handles files with CRLF (Windows) newlines and no final newline.

0.5.0 - 2020-10-09

Changed

  • [BREAKING] generate: Renamed --n-records to --record-count.

  • generate: --record-count is parsed as a u64 rather than an i32. The argument parser never allowed negative numbers, so this change still includes the entire previous input set.

0.4.0 - 2020-06-30

Added

  • The generate command adds a --seed <u64> option to seed the random number generator. This is useful to regenerate the same outputs.

Changed

  • The FASTQ generator now uses the Sanger/Illumina 1.8+ range of quality scores ([0, 41]). It samples scores on a normal distribution (μ = 20.5, σ = 2.61).

0.3.1 - 2019-08-14

Changed

  • Updated dependency bloom --> bbloom to reflect a name change in the library.

0.3.0 - 2019-08-09

Added

  • New filter command. This accepts an allowlist of record read names to keep in the output FASTQ.

  • Add Dockerfile to build a self-contained image for fq. Build with docker build --tag fqlib ..

  • Show git commit ID and date in display version, e.g., when using --version. This makes it easier to know the exact build of fqlib being used.

Changed

  • [BREAKING] generate: Renamed --num-blocks to --n-records.

0.2.0 - 2018-11-28

Added

  • For paired end reads, fq lint exits with unexpected EOF if the both streams do not finish together.

  • Multistream gzip files can be used as inputs. Written files still use a single stream.

  • fq lint can take one FASTQ file as input for only single read validation.

Changed

  • A single binary fq with subcommands replaces fqgen and fqlint. Update usages to fq generate and fq lint, respectively.

  • Metadata from CASAVA 1.8 read names is truncated. This is handled the same as interleaves.

Fixed

  • Fix line offset in error messages, which was previously off by 4.

0.1.0 - 2018-06-05

  • Initial release