Changelog¶
version 0.12.2¶
- new examples/ testsuites and tutorials, leading to development of new testsuites ebola-sierraleone14 and MTBC-SNP-barcodes
- new testsuite discovering/loading mechanism
- easier selection of testsuites via GUI
- better support for clonal variants
- MTBC/resistance scans pncA gene; mutations in rrsS and rrsK (ribosomal RNA) are labeled correctly
- summarize command
- added support for more .fastq.gz formats, including paired files
- increased test coverage
version 0.12.1¶
- support .fastq.gz files
- added new ways to load testsuites
- some bugfixes in scripts/table_{scan|combine}.py
- moved additional testsuites into their own repositories
version 0.11.3¶
- (first public version, pushed to github)
- compile on windows without having to install pthread files
- moved all testsuites into separate testsuite/ directory
- introduced testsuite compatability checks
- updated MTBC.resistance testsuite (added katG.279, rpoC.N698H, renamed rrsK)
version 0.11.2¶
- renamed to KvarQ (previous name was “pyseq”)
- made xlrd, xlwt optional dependencies (import/export data as .csv)
- polished GUI somewhat
version 0.11.1¶
- internally use kvarq.analyse.Coverage instead of kvarq.genes.Test to identify sequences and hits
- more compact file format
- support legacy .json files; legacy testsuites can also be loaded separately (some are included in testsuites/legacy/)
version 0.10.10¶
- enabled multiple use of same kvarq.genes.Test for different kvarq.genes.Testsuite
version 0.10.9¶
- implemented all plotting in Tkinter – matplotlib not needed anymore
- added settings dialog to GUI
- moved non-published tests into separate files in testsuites/ directory
version 0.10.8¶
- added new fields to stats : nseqhits, records_parsed
- added new attributes to kvarq.fastq.Fastq : readlength, records_approx
- (these fields are also displayed in the json explorer)
- added terminal color support
- improved FastQ quality score decoding
- improved scripts/table_combine.py (insert data into existing table)
- include html documentation in distributions
- testsuites can be loaded from arbitrary locations (see Rolling your own testsuite)
version 0.10.7¶
- relaxed .fastq file format specifications
version 0.10.6¶
- .fastq file format checking (both in kvarq.fastq and kvarq.engine)
- give every thread 10 file junks to keep scanning speed constant until the end
version 0.10.5¶
- “batch processing” in kvarq.gui.{simple|explorer}
- resistances output aa number
- cleaned up output spoligo/resistances
- do not include hits in .jsons when using gui/simple