ntEdit v2.1.1

Allow relative or absolute path when specifying reads prefix with --reads

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).