multiple alts, multiple lines, overwrite.

v0.2.7 (dev)

• restore multiple threads per annotation file after fix in biogo/hts (#64)
• add setid builtin to set the ID field and remove need for lua and fix some bugs.
• fix bug in self with multiple alternates when there were multiple overlaps (thanks Matthew).
• fix for #68, #69 -- with Number=A, op="self", the output will always have a number of elements
  equal to the number of alternates. If there are > 1 annos for a given site, later values will
  overwrite previous.

fixes for Number=A, op=self

• restore multiple threads per annotation file after fix in biogo/hts (#64)
• add setid builtin to set the ID field and remove need for lua and fix some bugs.
• fix bug in self with multiple alternates when there were multiple overlaps (thanks Matthew).
• fix for #68, #69

fix race

v0.2.6

• fix race condition from 0.2.4 by reverting some speed improvements from that release.

div2

v0.2.4

• 30-40% speed improvement when annotating with few, large files by parallelizing decompression.
• handle multiple values to div2 (mostly for multi-allelics)
• if _af or af_ is in the name then make Number=A for a postannotation.

FILTER and delete

v0.2.3

• allow pulling the 'FILTER' field from a VCF by specifing 'FILTER' in the fields
• add new op for postannotation only 'delete' which can be used to remove fields from the INFO.
• use Description from annotation as Description in annotated file (thanks @xuyangy for the implementation #43)

postannotation + ID fix

v0.2.2

• wholely fix order of error checking from postannotation (affects users using ID annotation) (thanks @vladsaveliev)

postannotation ID fix

v0.2.1

• correct order of error-checking on return from postannotation (affects users using ID annotation)

multiallelics!

This support brings full and proper support for multiallelics. Any annotation file and field that has Number=A in the header can be used to correctly annotate a query file with ops=['self'].
See: http://brentp.github.io/vcfanno/#multi-allelics for more details.

v0.2.0

• proper support for multi-allelics in query and in annotation with op="self"
• allow post-annotation to set ID column

v0.1.2-dev

add conf file for gnomad

fix END in non VCF files with ref and alt columns

v0.1.1

• set number=1 when op=min see #40
• fix when we get -0 converted to just '-' (#42)
• when an annotation bed file has a header with 'ref' or 'reference' and 'alt' or 'alternate',
  then match on the ref and alt values defined in those columns (not just on position as for bed).
• (vcfgo) allow double-digit number in header thanks @chapmanb
• correct END position when using ref and alt from a file with only a position (infer end as start + len(ref)) [thanks Tomas].
• about 15% performance improvement mostly due to go1.8