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CHANGELOG.md

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ChangeLog

A simple change log file to keep track on what is new.

Versions

  • 2.1 (NOT RELASED YET)

    • Proper handling of files with 0 entropy.

  • 2.0 (2015-05-22)

    • Fixing a ancient bug: remove carriage return characters from sample mapping files (so people who export their mapping files from EXCEL on Mac computers can get nice figures as well).

  • 1.9 (2015-03-31)

    • New script o-smart-trim to trim ragged ends of alignments with care.
    • Slightly better command line interface.
    • Minor bug fixes.

  • 1.7 (2015-01-20)

    • Incompatibility with pip 6.0.6 is fixed.
    • Minor bug fixes.

  • 1.6 (2014-11-30)

    • Minor bug fixes.

  • 1.5 (2014-11-11)

    • o-dist.R is removed from the codebase. Another script that computes pairwise distances of sequencs in a given FASTA file to generate a distance matrix is added (o-dist) along with another script to visualize this informatopn (o-visualize-distance-matrix.R).

  • 1.4 (2014-10-01)

    • A minor update to remove a once-useful command line parameter from the oligotyping pipeline, --gen-sample-oligo-networks. The same functionality is now available as a separate script (o-generate-oligo-base-networks). I thank Sinisa Bratulic for reporting it.

  • 1.3

    • A minor update to fix the broken backward compatibility of Django v1.7. I thank Bernd from Amsterdam for pointing it out.

  • 1.2

    • Bug in MANIFEST file is fixed.
    • Bug related to --quick flag (which resulted in under-estimaded benchmark scores) is fixed.

  • 1.1

    • ggplot2-related bug (which resulted in blank stackbar plots) is fixed.

  • 1.0

    • Minimum Entropy Decomposition is an part of the pipeline.
    • Experimental purity score implemented by Doğancan Özturan is now included in the HTML output.

  • 0.96

    • Improved HTML output.
    • Better error reporting.

  • 0.95

    • GEXF support. Now oligotyping pipeline generates Gephi (https://gephi.org/) compatible XML file for network analysis.
    • Bug fixes.

  • 0.9

    • Multithreading support. Oligotyping pipeline runs processes in parallel whenever it is possible.
    • More comprehensible HTML output.
    • RUNINFO.cPickle format has changed.

  • 0.8

    • Dependency to USEARCH is removed from the pipeline. NCBI's blastn is now the default search tool for relevant operations.
    • Reads that are being discarded during the noise removal step are now tracked to avoid biases.
    • New commandline parapmeter: --sample-mapping (which supports TAB delimited categorical mapping files for samples to be used for post-analysis visualizations; a relevant blog post: http://oligotyping.org/2013/02/04/basic-sample-mapping-with-oligotyping/).

  • 0.7

    • Major performance improvements.
    • All output matrices are transposed.

  • 0.6

    • New commandline parameter: --min-substantive-abundance (a very important new parameter for better noise control, see http://oligotyping.org/2012/09/18/command-line-parameters-explained/ for details).
    • New commandline parameter: --gen-oligotype-sets (oligotype sets are going to be generated only when requested).
    • New commandline parameter: --exclude-oligotypes.
    • Naming convention for agglomerated oligotypes has been changed; now they are known as oligotype sets.

  • 0.5

    • Grouping oligotypes based on their frequency patterns across datasets has been added to the pipeline.
    • Code directory structure has been changed.

  • 0.4

    • Visualization showing normalized oligotype distribution across datasets has been added to the pipeline.

  • 0.3

    • New commandline parameter: --colors-list-file.

  • 0.2

    • Unittests implemented for various functions
    • Class structure was improved

  • 0.1

    • Initial oligotyping library