ntEdit v1.3.4

support for IUPAC characters in snv (-s 1) mode

Better handling of IUPAC nucleotide codes in SNV mode; In that mode, IUPAC positions will be inspected for A,C,G & T (no just the base(s) not captured already by the IUPAC code as it is the case in polishing mode.

no degradation of performance, except for additional computing needed to inspect possible alternate base substitutions to IUPAC codes in SNV -s 1 mode

ntEdit v1.3.3

Support for IUPAC nucleotide codes (R,Y,S,W,K,M,B,D,H,V).

When ntEdit encounters a IUPAC nucleotide code other than A,C,G,T,N a base replacement will be made with possible alternate(s), only when a qualifying change is different than the base possibilities already captured by the code (e.g. Only a 'C' will be considered for replacing code D, which specifies A or G or T). This could be useful for evaluating missed SNVs (-s mode set), for instance but also in polishing mode where kmers with these codes will be inspected for alternative bases, filters permitting.

ntEdit v1.3.2

-Initial VCF output support

ntEdit v1.3.1

-detect k automatically (from Bloom filter header) / removed k parameter user input
-sort alternate bases by distinct decreasing kmer support
-streamline runtime messages

ntEdit v1.3.0

-minor bug fixes
-output alternate bases in changes.tsv when pass threshold x/X y/Y
-implement snv option for detecting single nucleotide variations (in kmers having similar context)
-implement secondary Bloom filter for filtering out certain kmers

ntEdit v1.2.3

-Ability to threshold on ratio of kmer subsets (-X and -Y parameters), which is more intuitive.
-Better control over the size of the kmer subset to apply X/Y or x/y thresholds on (-j jump parameter)
-Code clean up / azure integration tests

ntEdit v1.2.2

fixed a bug that caused rogue runs yielding large fasta outputs on some genome drafts / k combinations

ntEdit v1.2.1

minor bug fixes

ntEdit v1.2.0 C++

--> Improved memory scalability and cache performance with a change in data structure
--> Added 2 different modes for selecting the type of edit to be made at each position
--> Refined low complexity insertion detection
--> Add feature (-c) to cap insertions at a position to prevent stalling
--> Improve code readability

ntEdit v1.1.0 initial C++ version

The ntEdit v1.1.0 initial C++ version is the version tested in the ntEdit scientific manuscript