bed, custom js, API

v0.0.3

• custom ops with javascript. see example conf and custom javascript
• proper support for variants.
• option to annotate BED files. (this is automatic, just use a bed file as the query).
• vcfanno has an api so it can be use from other progs.

support for annotating the ends of variants (for CNVs and SVs)

This release adds much more test-coverage (>80%).

It also provides a feature for annotating large variants where we want to know about, e.g. the breakpoints of structural variants. If the -ends flag is specified from the command-line, then in addition to the annotation of the entire interval (as in the default mode), each variant will be annotated by what overlaps its 1-base left end (prefixed by "left_") and its 1-base right end (prefixed by "right_"). The left and right annotations are only done for intervals longer than 1-base.

It also adds the -permissive-overlap flag which tells vcfanno that any overlap is sufficient to add an annotation. In default mode, it requires that they also share the REF and at least 1 ALT allele. (this is used implicitly for the above -ends parameters).

initial release

initial release of vcfanno. binaries for linux, windows, mac 32/64 bit provided.