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CHANGELOG.md

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Change Log

All notable changes to Quasitools will be documented in this file.

0.7.0

Added

Commands:

  • complexity bam: measures the complexity of a quasispecies across a reference genome using aligned reads in BAM format

Options:

  • complexity: now has the option to filter out low frequency haplotypes

Changed

  • complexity has been replaced with complexity fasta and complexity bam
  • Fixed a complexity bug with haplotype counting and consensus sequence generation.
  • Fixed a complexity bug when parsing haplotypes with indels.

0.6.0

Changed

  • Integrated PyAAVF and changed output of mutation report in hydra command to produce AAVF file along with call aavar to produced AAVF file instead of HMCF file.
  • Made various changes to the documentation to improve clarity.
  • Fixed quasitools distance sometimes crashing because of uneven coverage.
  • Improved the execution time of quasitools distance.
  • Fixed the Hamming distance calculation using integers instead of floats, depending on the Python version.

0.5.1

Added

  • Use MkDocs for documentation

Changed

  • Make VCF dependency optional in aavar and add optional VCF dependency in codonvar
  • Fix hydra consensus output: exclude header line if there are no sequence lines
  • Remove a deprecated regular expression sequence in reference_parser.py

0.5.0

2018-09-25

Added

Commands:

  • complexity: measures the complexity of a quasispecies

Changed

  • Improved read parsing, pileup generation, and related interal data structures.

0.4.2

2018-07-25

Changed

  • Fix bug in quality_control where iteratively trimmed reads are not used when printing output file.

0.4.1

2018-07-24

Changed

  • Updated hydra command and quality command to fix boolean flag for enabling median or mean score cutoff value.

0.4.0

2018-06-29

Added

  • commands:
  • quality: performs quality control on FASTQ reads
  • modules:
  • quality_control.py: contains QualityControl class

Changed

  • Updated hydra command to use new quality control class, masking and/or trimming reads based on command-line options that user has specified.
  • Fixed bug in cmd_consensus.py which occured when there are multiple records in the reference file and the user is writing to a file.

0.3.1

2018-04-13

Added

  • Updated hydra command to accept an id to be used as the sequence identifier in the consensus report, and as the RG-id in the bam file

0.3.0

2018-04-10

Added

  • commands:
    • distance: returns the evolutionary distances between viral quasispecies as a distance matrix
  • modules:
    • pileup.py: contains Pileup and Pileup_List classes
    • distance.py: contains Distance_Matrix class

0.2.3

2018-03-16

Changed

  • Fixed FASTA identifier in consensus output for the consensus and hydra commands
  • User can pass in a default id as an option
  • RG tag is used if present in the supplied .bam file

0.2.2

2017-11-27

Changed

  • Updated samtools dependency to v1.3

0.2.1

2017-11-22

Changed

  • fixed call codonvar command to properly output to either file or stdout depending on flag

0.2.0

2017-11-03

Added

  • commands:
    • hydra: which identifies HIV Drug Resistance in a NGS sample
    • call: new base command for nt, aa, and codon variant calling
      • ntvar: formally just callntvar
      • aavar: formally aavariants
      • codonvar: reports codon variants for use with dnds command
    • dnds: calculates dnds values per coding region using codonvar output

Changed

  • Renamed aa_census command to aa_coverage
  • Hardended command options and parameters

0.1.0

2017-09-06

This is the initial release of Quasitools