v0.22.1

Added

• New fastlint program that applies the SDUST algorithm (taken from minimap2) to FASTQ data in order to filter reads with very low complexity. This is useful for screening out reads that cause issues with downstream tools such as Flye.
• fastcat now has a --dust option to filter reads using the fastlint functionality.

v0.22.0

Changed

• Bumped htslib to 1.21.

Added

• fastcat now has a verbose option. Logging of filepaths processed is suppressed without --verbose.

v0.20.0

Changed

• Tightened up checks on provided regions.
• Histogram files were not written when input was empty, they now are restoring previous behaviour.

Fixed

• Read mean quality was not recomputed when qs tag was not present in BAM.

v0.19.1

Fixed

• Compilation on macOS with clang.
• Segmentation fault with bad read group information.

v0.19.0

Added

• Regions can now be provided in a three (or more) column BED file to bamstats to calculate per-region statistics.

Fixed

• A segmentation fault whilst writing statistics files when demultiplexing is enabled.
• A memory leak occurring in bamstats when qcfail reads are encountered in the input.

Changed

• Retrieve mean quality score 'qs' tag from BAM record, rather than recomputing. Previous behaviour can be restored with the --recalc_qual option.
• Get basecall model version id from model_version_id in FASTQ header (in addition to basecaller_model_version_id)
• Parse required bam tags in one pass rather than piecemeal as required.

v0.18.6

Changed

• Ill advised parsing of RG ID field has been extended to additionally allow for protocol_run_id style (uuid) Run IDs, as well as standalone acquisition_id (sha1) Run IDs

v0.18.5

Changed

• Parsing of RG ID field containing a modified base model, now returns only the core basecaller model.

Fixed

• Workaround samtools "bug" where RG ID suffix is not fixed width.

v0.18.4

Fixed

• Segfault on SAM-style tags without values in the FASTQ header.

v0.18.3

Fixed

• Bug causing segfault on unlikely RG SAM tags in FASTQ header comments.
• SAM parsing of FASTQ header not enabled if only either of RG or RD tag is present and at the beginning of the header comment.

v0.18.2

Fixed

• 'run_id' instead of 'basecaller' as column name in bamstats basecaller summary output header line.