[Bioc-devel] Preparing package release notes
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")
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.
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Telephone: 206 667-2793
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