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Bioconductor Release v3.13
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@zhengxwen zhengxwen released this 11 Jun 00:15
· 141 commits to master since this release
v1.32.0
47d2a1f

CHANGES IN VERSION 1.32.0

NEW FEATURES

  • new option 'ret.idx' in seqSetFilter() for unsorted sample and variant indices
  • new option 'ret.idx' in seqSetFilterAnnotID() for unsorted variant index
  • rewrite the function seqSetFilterPos(): new options 'ref' and 'alt', 'multi.pos=TRUE' by default
  • new option 'packed.idx' in seqAddValue() for packing an indexing variable
  • new option 'warn' in seqSetFilter() to enable or disable the warning
  • new functions seqNewVarData() and seqListVarData() for variable-length data

UTILITIES

  • allow no variant in seqApply() and seqBlockApply()
  • the list object returned from seqGetData() always have names if there are more than one input variable names

BUG FIXES

  • seqGDS2VCF() should output "." instead of NA in the FILTER column
  • seqGetData() should support factor when '.padNA=TRUE' or '.tolist=TRUE'
  • fix seqGDS2VCF() with factor variables
  • seqSummary(gds, "$filter") should return a data frame with zero row if 'annotation/filter' is not a factor
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