1.2.5

Bug Fix

1. fix a minor problem when occasionally the common part of ref and alt allele contains concordant repeats which is not the repeat variants unit.
2. fix a bug for using csto as the cds length error in stoploss snv mutation annotation, which leads the error extent length.
3. For multi-aa synonymous variants, the anchor position is wrong, this might influence those rare mutations, update is recommended for all users.

Feature Added to meet the HGVS current naming rule.

1. Change getUnifiedVar to give absolutely left or right aligned result without consider the repeat elements when "norep" is set to 1.
2. add standard_cHGVS key for delXXXinsXXX format cHGVS annotation.
3. add standard_cHGVS for gene flanking region cHGVS annotation.

1.2.0

BedAnno 1.20 Release Note

Compare with 1.15 updates

Features updated

1. IO::Uncompress::Gunzip add option MultiStream => 1 to fit the need of version update of this package
2. Variant position and ref alt standardization method update to have the ablity to not to give rep format variant with left aligned, and this is used when querying public databases.

Issue Fixed

1. Change to give ext format pHGVS instead of fs format for stop-loss function variants.
2. Change to give 'stop-retained' function instead of 'no-change' to variants located at stop-codon region with neither AA change nor stop-codon effect change， and give the format like p.(*123=) pHGVS.
3. Fix issue when transcript-refgenome differences on the edge of exon where variants located at, give the most accurate prediction of functions.
4. Fix issue of gHGVS format string gives left aligned variant format problem.