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Changes In Version 0.2.0 (May 12, 2022)

  • Addressed issues 12, 14, and 19: refactored commands merge sortreads and filter to work with zipped files (.gz and .bz2 format).
    • Merge and sortreads produce zipped files when zipped files are provided: issues
    • filter can accept compressed input: issue 19,
    • sortreads produce compressed output when provided with compressed inputs: issue 14,
    • merge produce compressed output when provided with compressed: inputs 12.
  • Addressed issues 15, 16, 17, 18 (improved demultiplexing with sortreads):
    • implemented --no_reverse option to check only on strand: issue 15,
    • use cutadapt v3 to search all tags pairs in parallel: issue 16,
    • added options --tag_to_end and --primer_to_end to search and trim for tags (issue 17) and primers (issue 18) only at the end of the strands.
  • Addressed issue 20:
    • added command random_seq to produce random samples from a dataset
  • Addressed issue 1:
    • Integrated the make_known_occurrences command to create a .tsv file with the known occurrences.

Changes In Version 0.1.22 (Jan 31, 2022)

  • Updated and tested with python 3.9 and 3.10

Changes In Version 0.1.21 (Dec 11, 2020)

  • ENH added '--countreads' option to 'vtam pool'
  • ENH using OSF database for VTAM files
  • DOC
  • BUG bugs

Changes In Version 0.1.20 (Oct 15, 2020)

  • DOC
  • ENH Keep separated samples from different run in pooled asv table
  • BUG

Changes In Version 0.1.19 (Oct 10, 2020)

  • BUG fixed filter codon stop and wrapper tests
  • ENH Fixed used of LFS resulting in github fees

Changes In Version 0.1.18 (Sep 23, 2020)

  • BUG bugs fixed

Changes In Version 0.1.17 (Sep 19, 2020)

  • DOC Renamed and improved command-line interface help
  • ENH Added a 'vtam example' command to generate a file tree for a quick start

Changes In Version 0.1.16 (Sep 12, 2020)

  • DOC updated docs and doc files

Changes In Version 0.1.15 (Sep 10, 2020)

  • BUG Compatible biopython >= 1.78

Changes In Version 0.1.14 (Sep 8, 2020)

  • ENH Cluster sequences in ASV table
  • ENH Label keep occurrences in ASV table
  • RFR Renamed biosample to sample

Changes In Version 0.1.13 (Jul 12, 2020)

  • BUG fixed read fasta from sorted reads
  • ENH partially windows compatible

Changes In Version 0.1.12 (Jul 3, 2020)

  • BUG fixed FilterPCRerror runned with all variants

Changes In Version 0.1.11 (Jun 22, 2020)

  • ENH verification of --cutoff_specific and --lfn_variant_replicate arguments

Changes In Version 0.1.10 (Jun 18, 2020)

  • RFR Refactored optimize lfn variant or variant replicate
  • TST New tests optimize lfn variant or variant replicate

Changes In Version 0.1.9 (Jun 12, 2020)

  • BLD requirements.txt missing in build

Changes In Version 0.1.8 (Jun 12, 2020)

  • BUG Fixed that vtam must run again if --params file is updated (Mantis issues 0002620, 0002621)
  • ENH vtam coi_blast_db progressbar

Changes In Version 0.1.7 (Jun 8, 2020)

  • RFR vtam coi_blast_db refactor/added --blastdbdir BLASTDBDIR and --blastdbname BLASTDBNAME arguments

Changes In Version 0.1.6 (Jun 3, 2020)

  • BUG 0002609 Fixed lfn_variant(_replicate) cutoff specific
  • BUG Various bugs

Changes In Version 0.1.5 (Mai 31, 2020)

  • ENH: issue 0002607. check paramater names in params.yml
  • BUG: issue 0002606. When using --params in filter lfn_read_count_cutoff takes the value of lfn_sample_replicate_cutoff

Changes In Version 0.1.4 (Mai 29, 2020)

  • BUG: Fixed filter

Changes In Version 0.1.3 (Mai 27, 2020)

  • BUG: Fixed OptimizePCRerror

Changes In Version 0.1.2 (Mai 25, 2020)

  • Bug FilterMinReplicateNumber fixed

Changes In Version 0.1.1 (Mai 24, 2020)

  • Added tests
  • Refactored code
  • Change optimization based on explicit 'keep' and 'delete' variants

Changes In Version 0.1.0 (April 30, 2020)

  • Bugs fixed
  • Added tests
  • Created test dataset
  • Made faster some parts of the code

Changes In Version 0.0.1.4 (April 13, 2020)

  • Bugs fixed
  • Updated to use uchime3_denovo
  • Updated to use wopmars 11

Changes In Version 0.0.1.3 (April 7, 2020)

  • VariantReadCount: Fixed "insert variants"

Changes In Version 0.0.1.2 (April 5, 2020)

  • 'sortreads' based on cutadapt
  • 'filter' commands output to asvtable file instead to output directory
  • new 'global_read_count_threshold' that will stop variants below this parameter to entering the database

Changes In Version 0.0.1.1 (March 22, 2020)

  • Change subcommand "poolmarkers" to "pool"
  • Reorder optimize columns and other minor output improvements
  • Fixed FilterLFNreference
  • Renkonen filter does not run if only one replicate

Changes In Version 0.0.1 (March 18, 2020)

  • First version running until the end without apparent bugs affecting results