EsViritu v1.3.3

add:

• implemented feature request from #45 to properly support interleaved FASTQ reads.

What's Changed

• Interleaved read support, to v1.3.3 by @mtisza1 in #46

Full Changelog: v1.3.2...v1.3.3

EsViritu v1.3.2

Fixed pyproject.toml file to include sparkline files in distribution.

Full Changelog: v1.3.1...v1.3.2

EsViritu v1.3.1

Fix:

• Remove unescaped "%" in the argparse help message (caused bug when using --help).

Full Changelog: v1.3.0...v1.3.1

EsViritu v1.3.0 (new taxonomic assignment behavior)

Report generation updates:

• Locally-vendored sparklines for simpler installation.
• Locally-vendored Oswald font for simpler report generation.
• Additional fields (see below)

New alignment setting:

• "sense" sensitive alignment to improve alignment from more divergent genomes. However, increases computational burden and raises false-positive rate in some cases.

New taxonomic assignment behavior:

• Added a post-consensus step that aligns consensus genomes to reference DB.
• Resolves lowest commons ancestor and changes taxonomic assignment when appropriate.
• brings in new fields to output tables: adj_taxonomy, consensus_ref_identity

Miscellaneous:

• adding sample_ID to FASTA headers

EsViritu v1.2.2

Minor bug fixes.

What's Changed

• fix: rare no primary reads issue. reformat data-directory page. by @mtisza1 in #42
• Fix trim_filter function for unpaired reads by @lisalenafaye in #38

New Contributors

• @lisalenafaye made their first contribution in #38

Full Changelog: v1.2.1...v1.2.2

EsViritu v1.2.1

Fixed:

• minimap2 preset properly applied to 2nd and 3rd round of alignments to virus DB.

Full Changelog: v1.2.0...v1.2.1

EsViritu v1.2.0

Features:

• Adding esv_create_taxonomy and esv_combine_tax for custom DB creation. See instructions on the docs
• support for long reads - ONT or PacBio. see --minimap2-preset

Fix:

• Appropriate logic for "denominator" read count for all preprocessing possibilities
• replacing curl with url in google_fonts() check in R script for report generation
• pi calculation error

Performance Improvements:

• parallelize contigs stats with _calculate_contig_stats_from_bam(), bam_coverage_windows() #31
• improve clustering logic cluster_assemblies_by_read_sharing()
• samtools sort threading

What's Changed

• Merge pull request #30 from cmmr/v1_dev by @mtisza1 in #32
• Performance improvements by @mtisza1 in #33
• to v1.2.0 by @mtisza1 in #34

Full Changelog: v1.1.6...v1.2.0

EsViritu v1.1.6

• feature: add --outdir flag to summarize_esv_runs and incorporate this into relevant scripts.
• bump version to v1.1.6

What's Changed

• to v1.1.6 by @mtisza1 in #30

Full Changelog: v1.1.5...v1.1.6

EsViritu v1.1.5

What's Changed

• Add optional --dedup flag for PCR duplicate removal by @dhoconno in #27
• bump version to v1.1.4 by @mtisza1 in #28
• bumping to v1.1.5 by @mtisza1 in #29

New Contributors

• @dhoconno made their first contribution in #27

Full Changelog: v1.1.3...v1.1.5

EsViritu v1.1.3

• fix: read.table no longer breaks with records with "#" character #24
• add: readstats summary #23

What's Changed

• to v1.1.3 by @mtisza1 in #26

Full Changelog: v1.1.2...v1.1.3