0.5.0

• restructured into python package
• refactored code
• split out info into separate class
• account for multinucleotide variant consequences
• lowered minor allele frequency threshold
• added imprinting, X-linked over-dominant and mosaic modes of inheritance
• fixed problem loading singletons
• fixed problem with CNVs with missing MADL2R values

0.3.6

• shifted start_lost to loss-of-function consequences
• fixed bug where we missed long CNVs not in known genes
• CNVs now use the per-gene symbols when available
• turned on filtering using ExAC frequencies
• reworked removing variants based on polyphen predictions
  • now use per gene polyphen predictions
  • all variants with polyphen benign get removed, not just the
    ones in trios
• re-include compound hets in proband-only analyses
• fixed bugs that lead to missing DDG2P CNVs under various scenarios
• updated rules for CNVs overlapping syndrome regions
• exclude monoallelic and X-linked dominant variants with high
  ExAC allele frequencies
• exclude compound hets when proband-only where both hets are
  missense
• only include compound hets in trios when in trans
• fixed bug when checking if CNVs intersect known gene boundaries

0.3.5

• bug fix for CNV inheritance when analysing proband-only.
• include X-linked over-dominance mode of inheritance.
• fix bug when parsing ped files when only one parent is specified.
• numerous changes to proband-only filtering.
  • lower MAF threshold for monoallelic and X-linked dominant variants
    when analysing proband-only.
  • remove heterozygous variants from recessive genes when
    analysing proband-only.

0.3.4

• minor bug fixes for CNV filtering, and case with multi-allelic sites where the alleles affect different "genes"
• updated paths for new datafreeze in helper scripts

0.3.3

• include CNVs in filter output
• allow for alternate gene symbols to capture additional compound
  heterozygotes (useful when not using a list of known genes).

0.3.2

Don't exclude variants that fail VQSLOD threshold, as the variants that pass all other criteria but fail this aspect contain a sufficiently high proportion of reportable variants. This adds around 20% more inherited variants.

0.3.1

minor fix for variants with single consequence, no HGNC, but multiple HGNC_ALL

0.3.0

Allow for per-gene consequences

0.2.0

• exclude inherited male chrX variants with non-zero hemizygous counts in ExAC.

0.1.2

• include additional gene annotations when available
• drop the known genes overlap checking, since we have the additional gene annotations