/usr/lib/R/site-library/Rsamtools/NEWS is in r-bioc-rsamtools 1.16.1-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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-------------------------
NEW FEATURES
o asSam converts BAM files to SAM files
o razip, bgzip re-compress directly from .gz files
o yieldReduce through a BAM or other file, applying a MAP function
to each chunk and reducing the result to it's final representation
SIGNIFICANT USER-VISIBLE CHANGES
o bgzip default extension changed to '.bgz'
o seqinfo,BamFile-method attempts to return seqnames in 'natural'
order, e.g., chr1, chr2, ...
o yieldSize now works on BAM files queried with ranges. Successive
ranges are input until the total number of records first equals
or exceeds yieldSize..
o scanFa supports DNA, RNA, and AAStringSet return objects
BUG FIXES
o scanFa returns correct sequence at the very end of files
o razip compresses small files
o applyPileups no longer crashes in the absence of an index file
CHANGES IN VERSION 1.14.0
-------------------------
NEW FEATURES
o seqinfo(FaFile) returns available information on sequences and
lengths on Fa (indexed fasta) files.
o filterBam accepts FilterRules call-backs for arbitrary
filtering.
o add isIncomplete,BamFile-method to test for end-of-file
o add count.mapped.reads to summarizeOverlaps,*,BamFileList-method;
set to TRUE to collect read and nucleotide counts via countBam.
o add summarizeOverlaps,*,character-method to count simple file
paths
o add sequenceLayer() and stackStringsFromBam()
o add 'with.which_label' arg to readGAlignmentsFromBam(),
readGappedReadsFromBam(), readGAlignmentPairsFromBam(), and
readGAlignmentsListFromBam()
SIGNIFICANT USER-VISIBLE CHANGES
o rename:
readBamGappedAlignments() -> readGAlignmentsFromBam()
readBamGappedReads() -> readGappedReadsFromBam()
readBamGappedAlignmentPairs() -> readGAlignmentPairsFromBam()
readBamGAlignmentsList() -> readGAlignmentsListFromBam()
makeGappedAlignmentPairs() -> makeGAlignmentPairs()
o speedup findMateAlignment()
DEPRECATED AND DEFUNCT
o deprecate readBamGappedAlignments(), readBamGappedReads(),
readBamGappedAlignmentPairs(), readBamGAlignmentsList(), and
makeGappedAlignmentPairs()
BUG FIXES
o scanVcfHeader tolerates records without ID fields, and with
fields named similar to ID.
o close razip files only once.
o report tabix input errors
CHANGES IN VERSION 1.12.0
-------------------------
NEW FEATURES
o BamSampler draws a random sample from BAM file records, obeying
any restriction by ScanBamParam().
o Add argument 'obeyQname' to BamFile. Used with qname-sorted
Bam files only.
o Add readBamGAlignmentsList function for reading qname-sorted
Bam files into a GAlignmentsList object.
USER-VISIBLE CHANGES
o bamPath and bamIndicies applied to BamViews returns named
vectors.
o 'yieldSize' argument in BamFile represents the number of
unique qnames when 'obeyQname=TRUE'.
BUG FIXES
o completely free razip, bgzip files when done.
o sortBam, indexBam fail gracefully on non-BAM input.
o headerTabix on an open TabixFile no longer reads the first
record
o scanBcfHeader provides informative error message when header
line ('#CHROM POS ...') is missing
CHANGES IN VERSION 1.10.0
-------------------------
NEW FEATURES
o BamFile and TabixFile accept argument yieldSize; repeated calls
to scanBam and scanTabix return successive yieldSize chunks of
the file. readBamGappedAlignments, VariantAnnotation::readVcf
automatically gain support for yield'ing through files.
o Add getDumpedAlignments(), countDumpedAlignments(), and
flushDumpedAlignments() low-level utilities for manipulating
alignments dumped by findMateAlignment().
o Add quickBamCounts() utility for classifying the records in a BAM file
according to a set of predefined groups (based on the flag bits) and
for counting the nb of records in each group.
SIGNIFICANT USER-VISIBLE CHANGES
o scanBamFlag isValidVendorRead deprecated in favor of
isNotPassingQualityControls
o Rename makeGappedAlignmentPairs() arg 'keep.colnames' -> 'use.mcols'.
BUG FIXES
o close razip, bgzip files when done
o bamReverseComplement<- failed to return the updated object
o scanBcfHeader works on remote files
o allow asBam to work without warnings on header-only SAM files
o some bug fixes and and small performance improvements to
findMateAlignment()
o fix bug in readBamGappedAlignmentPairs() where fields and tags
specified by the user were not propagated to the returned
GappedAlignmentPairs object
CHANGES IN VERSION 1.8.0
------------------------
NEW FEATURES
o Add readBamGappedAlignmentPairs() (plus related utilities
findMateAlignment() and makeGappedAlignmentPairs()) to read a BAM
file into a GappedAlignmentPairs object.
SIGNIFICANT USER-VISIBLE CHANGES
o update samtools to github commit
dc27682f70713a70d4f31bca652cf78e00757da2
o Add 'bitnames' arg to bamFlagAsBitMatrix() utility.
o By default readBamGappedAlignments() and readBamGappedReads() don't
drop PCR or optical duplicates anymore.
BUG FIXES
o readBamGappedAlignments handles empty 'tag' fields
o scanTabix would omit variants overlapping range ends
o scanFa would segfault on empty files or empty ids
CHANGES IN VERSION 1.6.0
------------------------
NEW FEATURES
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 references
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.
SIGNIFICANT USER-VISIBLE CHANGES
o ScanBamParam argument 'what' defaults to character(0) (nothing)
rather than scanBamWhat() (everything)
o bamFlag returns a user-friendly description of flags by default
BUG FIXES
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.
CHANGES IN VERSION 1.4.0
------------------------
NEW FEATURES
o BamFile class allows bam files to be open across calls to
scanBam and friends. This can be helpful when wanting to avoid
repeated loading of the index, for instance.
o BcfFile, scanBcf, scanBcfHeader to parse bcftools' .vcf and .bcf
files. Note that this implements bcftools notions of vcf and bcf,
and are not fully compliant with vcf-4.0.
o asBam converts SAM files to (indexed) BAM files
o FaFile, indexFa, scanIndexFa, scanFa index and parse (indexed)
fasta files.
BUG FIXES
o scanBamFlag isValidVendorRead had reversed TRUE/FALSE logic
o Attempts to read too many records caught more gracefully.
o samtools output to fprintf() or calls to exit() are handled more
gracefully
CHANGES IN VERSION 1.2.0
------------------------
NEW FEATURES
o Update to samtools 0.1.8
o Update to samtools svn rev 750 (Mon, 27 Sep 2010)
o sortBam sorts a BAM file
BUG FIXES
o Attempts to parse non-existent local files now generate an error
o Reads whose last nucleotide overlaps the first of a range are
now scanned / counted.
o scanning / counting reads late in large Windows files is fast
o scanBam tag fields of type 'A' parsed correctly
CHANGES IN VERSION 1.0.0
-----------------------
SIGNIFICANT USER-VISIBLE CHANGES
o scanBam returns minus-strand reads in the manner presented in
the BAM file, i.e., as though on the positive strand. This occurs
in revision 0.1.34
o readBamGappedAlignments replaces readBAMasGappedAlignments
NEW FEATURES
o ScanBamParam() accepts 'tag' argument for parsing optional fields
o BamViews can be used with scanBam, countBam,
readBamGappedAlignments
BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)
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