v0.3.16

Added

• Read mean Qscore and alignment flag added to stats_from_bam output.
• Add option to filter_bam to keep unmapped reads that pass (non-alignment) filters.
• Enable multithreaded bam file reading and writing in filter_bam.

Changed

• Pin numpy<2.0.

v0.3.15

Added

• mini_align can take a bam as input and optionally retain all or subset of bam tags.

Changed

• Drop porechop dependency from pypi package due to blocking package uploads. Add warning to the user if porechop is called by mini_assemble but does not exist.

v0.3.14

Changed

• subsample_bam and coverage_from_bam now have unified read filtering options and logic.

Added

• filter_bam to filter a bam with the same logic used in subsample_bam.

Fixed

• subsample_bam was previously subsampling proportionally before filtering resulting in lower than expected depth.

v0.3.13

Changed

• subsample_bam: --force_low_coverage saves contigs with coverage below the target
• subsample_bam: --force_non_primary saves multimapping for the subsampled reads
• coverage_from_bam: --primary_only considers only primary reads when computing the depth
• bedtools: upgraded to v2.31
• porechop: switched to using Artic version

Added

• Option -C for mini_align to copy fastx comments into bam tags

Fixed

• Minor compatibility fixes to support pandas>=2.0

v0.3.12

Changed

• subsample_bam: --quality filtering now uses mean error probability, not mean of quality scores as previously.
• subsample_bam: enable filtering for proportional subsampling.

v0.3.11

Fixed

• Fix crashes in subsample_bam with alignment filtering and common_errors_from_bam
• assess_assembly -H uses correct output directory.
• Handling of comments in bed files.

Changed

• Added Q(sub) to summary output.
• Ported bed file handling from intervaltrees to ncls, speeding up assessment and multithreading efficiency.

v0.3.10

Fixed

• stats_from_bam: handle cigar strings using = and X instead of M.

Changed

• Include mapping quality in stats_from_bam output.

Added

• Handling of LRA bams in which NM tag is number of matches rather than edit distance.
• Added an option (-y) to assess_assembly and mini_align to include supplementary alignments.
• Added an option (-d) to mini_align and assess_assembly to select minimap2 alignment preset.
• Added accumulation of errors over a number of chunks (-a option in summary_from_stats and assess_assembly) to get better stats.
• Use -L option for minimap2.
• Updated versions of minimap2, samtools, bcftools, bedtools, seqkit in Makefile to the most recent ones.

v0.3.9

Fixed

• Reduced memory consumption of catalogue_errors.
• fast_convert qa now properly outputs a fasta file
• Fixed long_fastx --others option
• Fixed split_fastx fastq output

Added

• assess_homopolymers can use multiple threads

v0.3.8

Changed

• Install paftools.js from minimap2 and k8

v0.3.7

Changed

• Speed improvements to several benchmarking and analysis scripts

Fixed

• Quoted all variables in mini_align to handle spaces in inputs.