NEWS

Changes in version 1.5.3
+ If during the indexing step, user didn't use --gencode
  for a Gencode transcriptome file, tximeta will deal with
  this internally now by stripping all characters after the
  vertical bar `|`, in order to match long transcript names
  in the `quant.sf` files to the correct transcript names
  in the GTF.

Changes in version 1.4.0
+ tximeta will now pull down RefSeq seqinfo, using the
  dirname() of the GTF location, and assuming some
  consistency in the structure of the assembly_report.txt
  that is located in the same directory. Needs more
  testing though across releases and organisms.
+ expanded caching of ranges to exons and genes as well.
  Exons in particular take a long time to build from
  TxDb, so this saves quite a lot of time.
+ new 'addExons' function will add exons to trancript-level
  summarized experiments, by replacing transcript GRanges
  with exon-by-transcript GRangesList. Purposely designed
  only for transcript-level, see note in ?addExons
+ tximeta now also caches the transcript ranges themselves,
  rather than just the TxDb. This shaves extra seconds off
  the tximeta() call!
+ add 'skipSeqinfo' argument, which avoids attempting
  to fetch chromosome information (from UCSC) if set
  to TRUE.

Changes in version 1.1.18
+ Specifying gene=TRUE in addIds() when rows are
  transcripts will attempt to use a gene_id column
  to map the IDs. This usually gives a better mapping
  rate.

Changes in version 1.1.14
+ Cut off version number from Ensembl names only (not GENCODE)

Changes in version 1.1.13
+ Added 'cleanDuplicateTxps' argument, which does a lot of work
  for the user: it downloads the FASTA from the source, identifies
  duplicate transcripts (identical cDNA sequence) then looks to
  see if transcripts that are in the quantification files,
  but missing from the GTF, could be renamed from the list of
  duplicate transcripts such that they would be present in the GTF.

Changes in version 1.1.11
+ Added coding + non-coding combinations of Ensembl transcriptomes
  to the hash table. Must be in this order: coding, then non-coding.

Changes in version 1.1.9
+ Added support for dammit de novo transcriptomes.

Changes in version 1.1.6
+ Added summarizeToGene as a method, to avoid conflicts with tximport.

Changes in version 1.1.5
+ Added in Charlotte's code to split out GENCODE and Ensembl code
  for generating transcript ranges.