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Tags: aparton/ensembl-vep

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release/91.1

Merging postreleasefix/91 to release/91

* postreleasefix/91:
  add hardcoded frequency test variants
  fix var cache info error
  cat into sort prevents running out of memory
  subversion update
  check defined before sedding
  gene_symbol should be exempt from numberification in JSON output
  remove any whitespace crud from input
  freeze installed Bio-DB-HTS version, move other installed versions to top for clarity

release/91.0

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Merge pull request Ensembl#113 from willmclaren/release/91

freeze installed Bio-DB-HTS version, move other installed versions to…

release/90.10

fix when name is 0 in BED

release/90.9

Merging postreleasefix/90 to release/90

* postreleasefix/90:
  sub version update

release/90.8

Merging postreleasefix/90 to release/90

* postreleasefix/90:
  fix for nuking existing CSQ so to avoid leaving consecutive semi-colons
  cell_type is comma-separated flag, not a flag that can be given more than once
  subversion update
  allow for VCF INFO fields with no value
  allow to skip empty lines

release/90.7

Merging postreleasefix/90 to release/90

* postreleasefix/90:
  better checks for population names passed when using --check_frequency
  fix when selecting ExAC_Adj
  dont run coveralls on perl5.8 as it is no longer supported
  subversion update
  remove pipe from fields written to VCF, add some extra tests
  ensure VCF chunks dont have spaces
  subversion update
  patch up funcgen schema and others to avoid test fails
  test for duplicate transcript removal
  deal better with duplicates from otherfeatures db

release/90.6

subversion update

release/90.5

Merging postreleasefix/90 to release/90

* postreleasefix/90:
  subversion update
  add some extra fork-failure safeguards, checks and tests

release/89.9

subversion update

release/90.4

Merging postreleasefix/90 to release/90

* postreleasefix/90:
  subversion update
  check SYMBOL exists before sedding it