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CHANGES.md

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v0.2.1

  • bump stream-vbyte for performance annotating
  • fix #43 where output vcf would have Number=, unless number was specified in config.json

v0.2.0

  • skip non ACGT alts (@migbro #39)
  • grab description from input vcf and propagate to annotated VCFs (@dmiller15, @migbro #34, #35)

v0.1.9

  • report missing float as . (thanks @dmiller15 #32)

v0.1.8

  • better help message indicating how to output bcf/vcf.gz (thanks @dvg-p4)
  • fix missing value in cadd example (thanks @dvg-p4)
  • doc types (thanks @enormandeau)
  • handle big files (#30)

v0.1.7

  • add wiki page and more information about decomposing variants
  • clarify warning on non ACGT (#23)
  • better error messages on missing/bad zip file

v0.1.6

  • change VCF header (#19)
  • output fewer warnings for '*' and other alternate alleles (#22)

v0.1.5

  • fix build on OSX (#18 from @sstadick)
  • handle empty alts (#16 from @sstadick)
  • add script for converting dbNSFP -> VCF -> echtvar encode

v0.1.4

  • fix bug with filter not removing (not filtering) variants correctly.

v0.1.3

  • exit with error on multi-allelics (previously, only first allele was used) ( #11)
  • more docs on conf file (thanks @m-pauper)
  • fix compression error for very dense regions (#12)
  • fix error when using hts_set_threads more than once and after reading header (#12)

v0.1.2

  • fix #8. bug introduced for string values.

v0.1.1

  • support multiple echtvar files to echtvar anno. This makes it possible to annoate with, for example gnomad and dbsnp.
  • support string fields. This works for fields with a lowish number (max of thousands) of unique values.
  • support extracting FILTER field from annotation VCF. So now can annotate with, e.g. gnomad FILTER field via:
    {"field": "FILTER", "alias": "gnomad_filter"},
    
    in the json file for echtvar encode. "FILTER" is a special-case, all other fields are from the INFO.