Changes - vcfanno

v0.2.9

restore multiple threads per annotation file after fix in biogo/hts (#64)
new op 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.
new op by_alt that will have Number=A and will append multiple annotations for the same alternate (from the same file) and output them as pipe-delimited. e.g with 2 alts, it might look like: 0.111,0.222|0.333 when the 1st alternate has a single value and the 2nd alternate has 2 values.

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

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.

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)

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

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

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].

drastically reduce the warning message output.
add field=['DP2'] for bam files which reports number of forward and reverse reads overlapping a variant. value returned can be replicated with: samtools mpileup -A -x -Q 1 -q 1 -r chrom:pos-pos $bam
add op=sum
expose ref and alt to lua.

when op=self, pull Number from the annotation file (previously Number was always 1)
when op=concat or op=uniq user Number=.
when name ends with '_float' '_int' or '_flag' that is used to determine the Type in the output and that is then stripped from the name. So, e.g. with names=["af_esp_aa_float"] The resulting header will be:

##INFO=<ID=af_esp_aa,Number=1,Type=Float,Description=...

fix regression with CIPOS/CIEND when using -ends with structural variants. (Thanks to Liron for reporting)
fix bug with uniq not uniq-ing (Thanks Liron for reporting)
improve error messages from lua (Thanks Komal Rathi for the test-case provoking this change).
improve handling of multiple values (usually due to multiple alts) for max and min. Now, if we have, e.g. var1:SAS=0.22,0.33 and var2:SAS=0.25 then max will give 0.33. This change makes max and min recursive so they'll call themselves on nested slices. Thanks @snashraf for reporting.

allow using postannotation even if not all requested fields were found for a given variant.
restore ability to have bams as annotation files. Can pull mapq and coverage. See examples/conf.toml
fix regression where output was not in sorted order.
fix regression that resulted in "too many open files" error.
expand test-suite.
fix bug found when using max() op

restore ability to take query file from STDIN (no tabix required).
fix memory leak. memory use now scales with number of procs (-p).
added new op 'self' which should be used for most cases when matching on ref and alt as it determines the type from the annotation header and uses that to update the annotated header with the correct type.
new documentation site
[[postannotation]] allows modifying stuff in the query VCF after annotation (or instead). See examples on the documentation site.
convert scripting engine to lua from javascript
add CADD conversion script and example

better support for flags. e.g. can specify a flag from js by ending the function name with _flag
[irelate] error if intervals are out of order within a file.
-base-path argument replaces basepath in .toml file
[vcfgo] report all headers in original file.
integrated server to host annotations
-ends argument will now use CIPOS and CIEND to annotate the left and right interval of an SV. If CIPOS and CIEND are undefined for a given interval, the ends will not be annotated.
for MNPs, cadd score is reported as a list of max values (of the 3 possible changes) for each reference base covered by the event.
fix bug in CADD annotation and provide CADD v1.3 download
~25-30% speed improvement. from a modest laptop: annotated 10195872 variants in 28.97 minutes (351984.0 / minute)

allow natural sort (1, 2, ... 9, 10, 11 instead of 1, 10, 11 ..., 19, 2, 20) via flag
vcfgo: handle lines longer than 65KB major
vcfgo: fix error reporting
irelate: report warning when chroms out of order

performance improvements for Javascript ops with pre-compilation.
bam: annotate with mapq and seq for mapping-quality and sequence respectively.
api now returns a channel on which to recieve annotated Relatables
vcfgo: fix printing of INFO fields with multiple values (thanks to Liron for reporting).
vcfgo: fix writing of ##SAMPLE and ##PEDIGREE headers. (thanks to Liron)