NEWS.md

In brendanf/tzara: Cluster long amplicons using dada2 denoising on variable regions

tzara 0.0.11

• fixed a bug in cluster_consensus() with character inputs when names are not given.
• cluster_consensus() now gives a result for a single (non-NA) unique sequence, even if there are less than 3 copies.
• speed up cluster_conensus() by catching some cases where the alignment step can be skipped.

tzara 0.0.10

• extract_region() auto-detects the format of the output file, if given, from the name.
• Fixed a bug where extract_region() was not saving quality information from the input to an output "fastq" file when the input was a "fastq" file or QualityScaledXStringSet.
• Added argument "dir" to dadamap(), to specify the location of input files, if derepFastq() was originally called on a directory of files.
• fixed a bug with "seq_id" and "filename" not being passed correctly from dadamap.list() to dadamap.derep.
• has_alphabet() now works even if some of the input sequences are NA.

tzara 0.0.9

• Added arguments "seq_id" and "filename" to dadamap(), to make it more user-friendly. Use of add_dada_names() is now unnecessary.

tzara 0.0.8

• Added a NEWS.md file to track changes to the package.
• Breaking Change: Uniformly use the column name "seq_id" rather than "seq", "seq.id", or "seq_name" for unique sequence identifiers.
• Add support for DNAStringSet and QualityScaledDNAStringSet in extract_region().

brendanf/tzara documentation built on March 11, 2021, 5:40 a.m.