[med-svn] [r-bioc-genomicfeatures] branch upstream updated (db6b129 -> 5f7c220)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository r-bioc-genomicfeatures.

      from  db6b129   New upstream version 1.28.5+dfsg
       new  5f7c220   New upstream version 1.30.0+dfsg

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 DESCRIPTION                                        |  32 ++-
 NAMESPACE                                          |   9 +-
 NEWS                                               |  44 +++
 R/Ensembl.utils.R                                  |  70 +++--
 R/TxDb-SELECT-helpers.R                            |  15 +-
 R/TxDb-class.R                                     |  58 ++--
 R/TxDb-schema.R                                    |  20 +-
 R/coordinate-mapping-methods.R                     |   6 +-
 R/exonicParts.R                                    |  18 +-
 R/extractTranscriptSeqs.R                          |  62 ++---
 R/makeTxDb.R                                       | 180 ++++++------
 R/makeTxDbFromEnsembl.R                            | 301 +++++++++++++++++++++
 R/makeTxDbFromGRanges.R                            |  70 ++++-
 R/transcriptsByOverlaps.R                          |  12 +-
 build/vignette.rds                                 | Bin 292 -> 293 bytes
 inst/doc/GenomicFeatures.R                         |  67 +++--
 inst/doc/GenomicFeatures.Rnw                       |  57 ++--
 inst/doc/GenomicFeatures.pdf                       | Bin 166472 -> 214029 bytes
 inst/extdata/GFF3_files/a.sqlite                   | Bin 247808 -> 286720 bytes
 .../GFF3_files/dmel-1000-r5.11.filtered.sqlite     | Bin 45056 -> 69632 bytes
 .../extdata/GTF_files/Aedes_aegypti.partial.sqlite | Bin 66560 -> 98304 bytes
 inst/script/makeTxDbs.R                            |  92 ++++++-
 man/DEFAULT_CIRC_SEQS.Rd                           |   3 +-
 man/TxDb-class.Rd                                  |  23 +-
 man/coordinate-mapping-methods.Rd                  |   3 +-
 man/coverageByTranscript.Rd                        |  19 +-
 man/disjointExons.Rd                               |  11 +-
 man/exonicParts.Rd                                 | 163 +++++++++++
 man/extractTranscriptSeqs.Rd                       |   8 +-
 man/extractUpstreamSeqs.Rd                         |  19 +-
 man/makeTxDb.Rd                                    |  40 +--
 man/makeTxDbFromBiomart.Rd                         |  34 +--
 man/makeTxDbFromEnsembl.Rd                         |  79 ++++++
 man/makeTxDbFromGFF.Rd                             |   6 +-
 man/makeTxDbFromGRanges.Rd                         |  14 +-
 man/makeTxDbFromUCSC.Rd                            |  11 +-
 man/transcriptLengths.Rd                           |  21 +-
 man/transcripts.Rd                                 |  33 +--
 man/transcriptsBy.Rd                               |  10 +-
 man/transcriptsByOverlaps.Rd                       |  59 ++--
 vignettes/GenomicFeatures.Rnw                      |  57 ++--
 41 files changed, 1279 insertions(+), 447 deletions(-)
 create mode 100644 R/makeTxDbFromEnsembl.R
 create mode 100644 man/exonicParts.Rd
 create mode 100644 man/makeTxDbFromEnsembl.Rd

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