CHANGES IN VERSION 1.6.0
------------------------

NEW FEATURES

    o add makeStandardTxDbsToSqlite() recipe

    o add 'ensembl' and 'MySQL' as possible SourceType values

    o tidy and export makeStandard*ToAHMs and makeNCBIToOrgDbsToAHMs

MODIFICATIONS

    o move currentMetadata

    o tidy pushResources interface

    o modified parsing of species name and genome in .ensemblMetadataFromUrl()

    o modified standard OrgDb recipe

    o enhance and clean vignette

    o move 'Tags' check from readCsvFromMetadata() to
    makeAnnotationHubMetadata()

    o remove dependency on xml2, curl, httr and probably other wheel
    reinventions, alter imports and suggests

    o specify multiple 'Tags' as colon separated string instead of comma
    separated; avoids problems with read.csv()

    o select data moved to GenomeInfoDbData package 

    o Added additional documentation instructions for core members to add
    contributed data to AnnotationHub
    
    o rename files; remove old JSON test file no longer applicable

    o pass 'install' argument down through recipe

    o General code tidy; remove unused functions and comments; clarify checks

BUG FIXES

    o readMetadataFromCsv() fills in DataProvider and Coordinate_1_based if missing

    o fix bug introduced in checking 'release' in makeEnsemblTwoBit recipe

    o makeAnnotationHubMetadata() now processes all inst/extdata/*.csv files

    o fix subset and import bug in makeAnnotationHubMetadata()

    o Fix bug in Rdatapath and sourceurl for makeEnsemblFasta.R

CHANGES IN VERSION 1.4.0
------------------------

NEW FEATURES

    o add script to generate user-contributed resources

    o makeEnsemblGtfToGRanges() no longer stores data in S3 but downloads
      and converts to GRanges on the fly

    o add EnsemblFastaTwoBitToAHM unit test

    o add man page for makeEnsemblTwoBitToAHM and
      ensemblFastaToTwoBitFile

    o add makeAnnotationHubMetadata() helper

MODIFICATIONS

    o move GSE62944-related code to ExperimentHub

    o move old vignettes to inst/scripts; add 'Introduction to
      AnnotationHubData' vignette

    o remove fasta and towbit files on the fly

    o add 'uploadToS3' argument to pushResources() and runRecipes()

    o move readMetadataFromCsv() from ExperimentHubData to
      AnnotationHubData

    o add 'fileName' arg to readMetadataFromCsv(); don't warn when
      'Tags' are provided

    o specify length for args in readMetadataFromCsv()

    o makeAnnotationHubMetadata() populates PreparerClass with package name

    o add 'fileName' arg to makeAnnotationHubMetadata()


CHANGES IN VERSION 1.2.0
------------------------

NEW FEATURES

    o add makeEnsemblTwoBit()

    o add hubError(), hubError<- generics and methods

    o create 'HubMetadata' class which 'AnnotationHubMetadata' inherits from

MODIFICATIONS

    o export ensemblFastaToTwoBitFile()

    o modifications due to changes in httr::HEAD():
      - AFAICT httr::HEAD() >= 1.1.0 accepts https only, not ftp
      - use xml2 instead of XML for parsing (httr >= 1.1.0 dependency change)

    o work on recipes:
      - clean up ChEA and Gencode
      - don't export tracksToUpdate(); was broken and not used
      - reorg man pages; combine Ensembl Fasta and TwoBit on single man page

    o work on updateResources():
      - push data to S3 before inserting metadata in db
      - isolate pushResources() and pushMetadata() from updateResources()
      - NOTE: Epigenome unit test is failing due to bad url. If not fixed by
        the host the recipe will need to change.

    o update makedbSNPVCF() to look in new clinvar location

BUG FIXES

    o fix bugs in makedbSNPVCF() recipe related to genome and tags


CHANGES IN VERSION 1.0.0
------------------------

BUG FIXES

    o ENSEMBL recipes discover gtf files on Windows.


CHANGES IN VERSION 0.0.214
--------------------------

NEW FEATURES

   o Have added vcf files from the following genome builds for humans
    "human_9606/VCF/clinical_vcf_set/",
    "human_9606_b141_GRCh37p13/VCF/",
    "human_9606_b142_GRCh37p13/VCF/",
    "human_9606_b142_GRCh37p13/VCF/clinical_vcf_set/"

   o For each genome build, where available, the following VCF file 
     formats are available
     a) all.vcf.gz
     b) all_papu.vcf.gz
     c) common_all.vcf.gz
     d) clinvar.vcf.gz
     e) clinvar_papu
     f) common_and_clinical 
     g) common_no_known_medical_impact

   o The user can refer to 
     http://www.ncbi.nlm.nih.gov/variation/docs/human_variation_vcf/
     for VCF file type formats