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.

v0.18.1

Fixed

• 'run_id' instead of 'basecaller' as column name in basecaller summary output header line.
• (null) in FASTQ header comments when run with -H on files that had basecall_model_version_id=... as only header comment.

v0.18.0

Added

• Basecaller summary information similar to runid summary.
• RNA poly-A tail length histogram output.

Fixed

• Random output for runid when not found in header.