CHANGES IN VERSION 1.3.5
-----------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o The default chimera removal method is now "consensus" in the removeBimeraDenovo function (method="consensus").

    o The filtering functions now remove phiX by default (rm.phix=TRUE).


CHANGES IN VERSION 1.3.4
-----------------------

NEW FEATURES

    o filterAndTrim is the new multithreaded interface for filtering and trimming. It is R-vectorized, in that it accepts vectors of input/output files. Supports both single-read and paired-read filtering.
    
SIGNIFICANT USER-VISIBLE CHANGES

    o Consensus chimera removal now supports multithreading.

    o The new trimOverhang option in mergePairs allows the portion of paired reads that overhang the start of the other read to be removed when merging.

    o Faster filtering by not enforcing redundant filtering conditions.

CHANGES IN VERSION 1.3.3
-----------------------

NEW FEATURES

    o ITS support. The dada method now handles variable-length amplicons, which allows common ITS sequencing strategies to be processed. Taxonomic assignment against the UNITE database is also now available.
    
SIGNIFICANT USER-VISIBLE CHANGES

    o The xxxFilter methods now have maxLen and minLen filtering parameters.

CHANGES IN VERSION 1.3.2
-----------------------

NEW FEATURES

    o learnErrors is a new method for learning error rates from a targeted number of reads. This wraps pre-existing functionality -- dada(..., selfConsist=TRUE) -- in a much easier to use form.
    
    o assignTaxonomy is multithreaded (multithread=TRUE) and can individually test reverse-complemented sequences and use them to classify if they better match the reference (tryRC=TRUE).

CHANGES IN VERSION 1.3.1
-----------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o The xxxFilter methods now (invisibily) return the number of reads that went in and that passed the filter.

    o fastqFilter now has a maxLen parameter, primarily for filtering/trimming 454 data.

BUG FIXES

    o trimLeft is now enforced before any filtering is performed.

    o Rscript invocations should now work without requiring an initial library(methods) call.

CHANGES IN VERSION 1.1.7
-----------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o The isBimeraDenovoTable method is now available through the convenience interface removeBimeraDenovo(..., tableMethod="consensus").

    o The vectorized Needleman-Wunsch algorithm is now available through nwalign(..., vec=TRUE). This aligner is very fast for short sequences, but performs no overflow checking so use on longer sequences (2kb+) with care.

BUG FIXES

    o It is now more difficult to mess up the internal structure of dada-class and derep-class objects.

CHANGES IN VERSION 1.1.6
-----------------------

NEW FEATURES

    o isBimeraDenovoTable is a new function for detecting chimeras on multi-sample sequence tables. It first identifies bimeras on a per-sample basis, and then uses a consensus approach to identify bimeric sequences. This improves the specificity of bimera classification for datasets with many samples.
    
SIGNIFICANT USER-VISIBLE CHANGES

    o The filenames is now included in the plotQualityProfile plot.

BUG FIXES

    o assignTaxonomy now works for sequences containg Ns.

    o Bimera detection now correctly handles non-unique sequences in the input.

    o Fixed a memory leak when using the HOMOPOLYMER_GAP_PENALTY option.

    o Warnings and errors during error estimation from small samples in the dada(…) function are now handled appropriately.


CHANGES IN VERSION 1.1.4
-----------------------

NEW FEATURES

    o Multithreaded chimera detection. The isBimeraDenovo(...) function is now multithreaded. This behavior is controlled by the multithread argument to the function, and is FALSE by default.

CHANGES IN VERSION 1.1.3
-----------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o The vectorized aligner has been updated. It is now more flexible, handling different length sequences and variable end-gap penalties. It is also faster: On default settings the dada(...) function is now 15-25% faster, and isBimeraDenovo is 2-4x faster.

CHANGES IN VERSION 1.1.2
-----------------------

NEW FEATURES

    o Species-level taxonomic assignment. The new assignSpecies(...) function uses exact matching to assign sequences to the species level. Currently a valid species training fasta is only available for the RDP taxonomic database.
    
CHANGES IN VERSION 1.1.1
-----------------------

BUG FIXES

    o Fixed the memory leak in isBimeraDenovo and friends.

    o Sequence tables are now integer rather than numeric.


CHANGES IN VERSION 1.1
-----------------------

NEW FEATURES

    o Multithreading. The dada(...) function is now multithreaded. This behavior is controlled by the multithread argument to the function, and is FALSE by default.
    
SIGNIFICANT USER-VISIBLE CHANGES

    o The phiX removal functionality in fastqFilter/fastqPairedFilter is now substantially faster.

BUG FIXES

    o Certain diagnostic return values of dada(..., pool=TRUE) are now appropriately constructed.

    o A 2-5% speedup from switching to C++11 hashed containers.

CHANGES IN VERSION 1.0
-----------------------

NEW FEATURES

    o The dada2 package is now available from Bioconductor (http://bioconductor.org)


CHANGES IN VERSION 0.99.9
-----------------------

NEW FEATURES

    o fastqFilter and fastqPairedFilter can now remove phiX contamination if rm.phix argument set to TRUE


CHANGES IN VERSION 0.99.8
-----------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Banding in nwalign is now turned off by default

BUG FIXES

    o Graceful handling of sequences which are not classified at any level by assignTaxonomy


CHANGES IN VERSION 0.99.7
-----------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o isBimera was rewritten in C, significantly increasing speed

BUG FIXES

    o An edge case bimera detection bug was fixed


CHANGES IN VERSION 0.99.6
-----------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Function documentation was reviewed and revised throughout the package


CHANGES IN VERSION 0.99.5
-----------------------

NEW FEATURES

    o plotQualityProfile displays a visual summary of the quality scores over sequences in a fastq file
    
    o removeBimeraDenovo conveniently identifies and removes chimeras from the input unique sequences

SIGNIFICANT USER-VISIBLE CHANGES

    o The dada2 package is now part of the devel branch of Bioconductor (http://bioconductor.org)

BUG FIXES

    o assignTaxonomy now handles varying levels of taxonomic classification in the training data


CHANGES IN VERSION 0.10.7
-----------------------

NEW FEATURES

    o dada2 now supports 454 pyrosequencing. When calling the dada function on 454 data, we recommend
       using the parameters USE_QUALS = FALSE, HOMOPOLYMER_GAP_PENALTY = -1, BAND_SIZE = 32

SIGNIFICANT USER-VISIBLE CHANGES

    o mergePairs is now "vectorized" over lists of input dada-class and derep-class objects

    o Added a homo_gap argument to nwalign which sets the homopolymer gap penalty in the N-W alignment

BUG FIXES

    o assignTaxonomy now uses less memory



