Changelog

El_gato:

• Fixed #23 mistake in locus locations used for depth calculations
• Fix bug in selecting neuA reference to use when more than one has coverage across the whole locus

Report script:

• Formatting and wording improvements

Documentation

• Lots of reorganization and improvements

Bugfixes:

• Fix #22 Use extended regex instead of PCRE to grab isPCR version information.
• Fix issue where el_gato would fail with KeyError if any SBT loci had 0 depth.

Improvements

• Improve detail of information about coverage/depth in the report output.

Bugfix:

Hard code version in el_gato.py script to fix bioconda build issues stemming from importlib metadata issues.

Changelog

Report script:

• Increase backwards compatibility by handling missing fields in json report. Missing fields populated with "-" in report pdf.
• Added optional disclaimer as a footer in the report

El_gato:

• Adjust minimum mapped reads to 10. If fewer than 10 reads are mapped el_gato aborts and reports that the ST cannot be determined.
• Fixed JSON report not generating when run is aborted.
• Added command line control over minimap k-mer size setting using -k, --kmer-size.

Changelog

Report script:

• el_gato version used for each sample now included on sample pages of report
• Make header optional. controlled with -n, --no_header.
• Removed image from header
• Support providing custom header as a string in command using --custom_header
• Support providing custom header in a text file using --header_file
• Header spacing now automatically determined using header size

El_gato:

• Include version number in the report.json
• Fix bug that caused locus headers to be included in the report if el_gato was run with -e

Bugfix

Bump version to fix version printing not reflecting installed version

Bugfix

Fix #17 - increased max_target_seqs setting of blastn to allow for larger database size.

Changelog

Report script:

• Add proper CLI interface
• Remove highlighting for problem results
• Add allele length to locus location table
• Add minimum depth and number of bases below depth threshold to read mapping table
• Add CLI option to abbreviate sample and contig names for better table appearance
• General style improvements and typo corrections

El_gato:

• Add better logic for handling user-provided DB. Should perform as expected now
• Add minimum of 5 depth of major allele for identifying primary mompS locus when only 1 read maps to minor allele
• Error out on wrong Python version
• Fix bug that sometimes causes ST 1724 to be incorrectly called as 1241
• Minor changes to style

SBT database:

• Update to May 2024 version
• Remove unneeded files

bugfix only check read files when reads provided.

Bugfix: print correct version when run with -v or --version