ntEdit v2.1.0

Added ntStat to the run-ntedit pipeline (replacing ntHits) for generating the Bloom filters used by ntedit
Added a parameter -e to run-ntedit for controlling the false positive rate of the ntStat Bloom filters

ntEdit v2.0.3

Refactoring to ntedit_run_pipeline.smk to ensure compatability with snakemake versions 8.17.0+ (#66)

ntEdit v2.0.2

Add support for cross-referencing indels with -l
Fixes to reporting indels in the VCF and changes.tsv output
Fixes to cross-referencing variants when -l specified
Add support for using fasta files with --reads
Add -l option to run-ntedit polish
Bugfixes to run-ntedit

ntEdit v2.0.1

Changed --draft argument for run-ntedit snv to --reference

ntEdit v2.0.0

New driver script run-ntedit to simplify running ntEdit
Add option to use genomes (--genome) in SNV mode instead of read sets
Support btllib Bloom and counting Bloom filters
Support zipped vcf
Fixed a bug that only reported variants with equal or greater k-mer support than reference base
Fixed a bug that could cause a segmentation fault when checking for deletions

ntEdit v1.4.3

Add missing include statement for mac
Versions 1.4+ add support for input VCF to cross-reference variants

ntEdit v1.4.2

VCF input to help identify variants of clinical significance
Includes option to supply a VCF input file to ntEdit, for cross-referencing base variants
For instance, users may wish to identify annotated clinical variants (e.g., ClinVar) in their genomics datasets, together with the -s 1 option
*To make the ntEdit output VCF easier to parse, v1.4.2 replaced the delimiter from pipe | to caret ^ since clinvar records have both pipes | and semicolons ; in their VCF INFO descriptions

ntEdit v1.4.1

VCF input to help identify variants of clinical significance
Includes option to supply a VCF input file to ntEdit, for cross-referencing base variants
For instance, users may wish to identify annotated clinical variants (e.g., ClinVar) in their genomics datasets, together with the -s 1 option

ntEdit v1.3.5

This release implements a new option (-a), which controls soft-masking (lower case) nucleotides in the supplied input [draft genome] sequence when its kmers are not found in the primary Bloom filter, and with no possible fix found in that filter (and optionally within a coverage slice provided by the secondary Bloom filter).

This option can be useful for identifying unresolved genomic regions, those with no equivalent in the supplied Bloom filter(s).

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