[Bioc-devel] Preparing package release notes

Martin Morgan mtmorgan at fhcrc.org
Fri Oct 21 23:45:19 CEST 2011

Package developers --

Each Bioconductor release is accompanied by release notes that mention 
new packages and other significant project developments. For the 
forthcoming release we would also like to include release notes for 
individual packages, so that users have an easy way to survey changes in 
their favorite packages.

To have your package release notes made available in the Bioconductor 
release notes, please arrange for your package to include a NEWS.Rd or 
NEWS file that can be parsed by the utils::news function. We'll run this 
command over all packages, using a 'query' argument that captures all 
updates more recent than the start of the current release cycle. For 
instance, Rsamtools in the devel branch is at version "1.5.76", so we'll 
get news with

 > utils::news(Version >= "1.5.0", "Rsamtools")

resulting in

Changes in version 1.6.0:


     o   TabixFile, indexTabix, scanTabix, yieldTabix index (sorted,
	compressed) and parse tabix-indexed files

     o   readBamGappedReads(), bamFlagAsBitMatrix(), bamFlagAND()

     o   Add use.names and param args to readBamGappedAlignments();
         dropped which and ... args.

     o   PileupFiles, PileupParam, applyPileup for visiting several BAM
	files and calculating pile-ups on each.

     o   Provide a zlib for Windows, as R does not currently do this

     o   BamFileList, BcfFileList, TabixFileList, FaFileList clases
	extend IRanges::SimpleList, for managings lists of file

     o   razfFa creates random access compressed fasta files.

     o   count and scanBam support input of larger numbers of records;
	countBam nucleotide count is now numeric() and subject to
         rounding error when large.

     o   Update to samtools 0.1.17

     o   asBcf and indexBcf coerces VCF files to BCF, and indexes BCF

     o   Update to samtools 0.1.18

     o   scanVcf parses VCF files; use scanVcf,connection,missing-method
	to stream, scanVcf,TabixFile,*-method to select subsets. Use
	unpackVcf to expand INFO and GENO fields.


     o   scanBam (and readBamGappedAlignments) called with an invalid or
	character(0) index no longer segfaults.

     o   scanBcfHeader parses values with embedded commas or =

     o   scanFa fails, rather than returns incorrect sequences, when file
	is compressed and file positions are not accessed sequentially

     o   scanBcf parses VCF files with no genotype information.

     o   scanBam called with the first range having no reads returned
	invalid results for subsequent ranges; introduced in svn r57138

     o   scanBamFlag isPrimaryRead changed to isNotPrimaryRead,
	correctly reflecting the meaning of the flag.

See ?news for more detail. We will collate these files no later than 
Friday, October 21.
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793

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