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

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