CHANGES IN VERSION 1.19.0
------------------------

INTERNAL BUG CORRECTION

    o 1.19.2 Update Metadata from Ensembl function to use
    GenomeInfoDb:::fetch_species_index_from_Ensembl_FTP instead of parsing the
    file path
    o 1.19.1 misplaced ! clause
 

CHANGES IN VERSION 1.17.0
------------------------

MODIFICATIONS

    o 1.17.3 add check for valid Title and Description in metadata file. It
    should not be empty or NA
    o 1.17.2 add XML as valid source type
    o 1.17.1 add GSEMatrix as valid source type

CHANGES IN VERSION 1.15.0
------------------------

MODIFICATIONS

    o 1.15.13 Added "BLOB" as a valid source type
    o 1.15.7 Added "MTX" as a valid source type
    o 1.15.6 Expanded documentation to clarify that data can be hosted
    publically not strictly Bioconductor AWS
    o 1.15.4 Added "XLS/XLSX" as valid source type

INTERNAL BUG CORRECTION

    o 1.15.11 updated GencodeGFF recipes for potential future use (still would
    revisit this with another update to do like ensembl on the fly)
    o 1.15.5 remove validity check that is wrong/outdated
    o 1.15.1 needToRerunNonStandardOrgDb added as helper function for when
    generating non standard org dbs. 1.15.3 added try catch in case aws buckets
    unreachable. 

CHANGES IN VERSION 1.13.0
------------------------

NEW FEATURES

    o Added ability to have multiple RDataPaths associated with single hub
    id for strongly associated files (like bam and its bai index file)
    o DispatchClass are now validated against AnnotationHub::DispatchClassList()
    which contains currently available DispatchClass and brief description of
    loading process.

CHANGES IN VERSION 1.11.0
------------------------
MODIFICATIONS

    o Removed scripts for Pazar DB as website no longer active
    o Update from BiocInstaller to BiocManager

NEW FEATURES

    o Species and taxonomyId are now validated against GenomeInfoDbData object

BUG FIX

    o Fix TwoBit resource receipe. Converts DNA that is not A,C,T,G,N to N do to
    design of rtracklayer::export for TwoBit
    o Fix bug with assignment of tags in annotationhub
    o makeEpigenomeRoadMap recipe updated to account for XML bug that cannot
    handle http urls. updated to https

CHANGES IN VERSION 1.10.0
------------------------
MODIFICATIONS

    o Moved readMetadataFromCsv back to AnnotationHubData.

    o Use AnnotationHubData::makeAnnotationHubMetadata to validate metadata.csv

    o readMetadataFromCsv is now internal function


CHANGES IN VERSION 1.8.0
------------------------

NEW FEATURES

    o Instead of using dropbox or ftp to deliver contributed resources to
    Bioconductor Core, temporary access to Annotation-Contributor user on S3 is
    utilized.

MODIFICATIONS

    o Modified readMetadataFromCsv; make RDataPath mandatory entry and if
    location_prefix is Bioconductor S3 bucket the Rdatapath must start with the
    package name

BUG FIXES

    o Add garbage collection to fix twobit memory allocation error

    o Fix files not deleting do to special characters in file names

    o Import dbGetQuery from DBI

    o Remove hard coded biocVersion in unit tests

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
