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NEWS
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CHANGES IN VERSION 2.16
-----------------------
NEW FEATURES
o (v 2.15.1) sortBam() gains support for sorting by tag (byTag) and using
multiple threads (nThreads). (See
https://github.com/Bioconductor/Rsamtools/issues/46. ; kriemo)
CHANGES IN VERSION 2.10
-----------------------
DEPRECATED AND DEFUNCT
o (v 2.9.1) Deprecate applyPileups() in favor of pileup().
CHANGES IN VERSION 2.8
----------------------
NEW FEATURES
o (v 2.7.2) idxstatsBam works on remote (e.g., http://) files and reports
unmapped ('seqnames' equal to *) reads. See
https://support.bioconductor.org/p/9136222.
CHANGES IN VERSION 2.4
----------------------
BUG FIXES
o (v 2.3.2; from v 2.2.2) Correctly handle '*' ('unknown') RNAME
during paired-end processing. See
https://github.com/Bioconductor/Rsamtools/issues/16.
o (v 2.3.5) Fix regression introduced by v 2.3.2
NEW FEATURES
o (v 2.3.1) Don't require BAM files to have @SQ lines; allows
parsing PacBio 'unaligned' BAM files.
(https://github.com/Bioconductor/Rsamtools/issues/15 ; jayoung)
CHANGES IN VERSION 2.0
----------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Migrate Rsamtools to Rhtslib. See Rsamtools/migration_notes.md for
more information about this migration.
o Remove unused fields from BamRangeIterator
o Remove BAM header hash init for pileup (already memoized in Rhtslib)
CHANGES IN VERSION 1.34
-----------------------
BUG FIXES
o (v 1.34.1) indexFa,FaFile-method correctly updates the index path.
CHANGES IN VERSION 1.33
-----------------------
NEW FEATURES
o (v 1.33.4, 1.33.7) scanBamFlag() gains isSupplementaryAlignment
support.
BUG FIXES
o (v 1.33.1) Do not try to grow NULL (not-yet-encountered) tags
(https://support.bioconductor.org/p/110609/ ; Robert Bradley)
o (v 1.33.5) Check for corrupt index
(https://github.com/Bioconductor/Rsamtools/issues/3 ; kjohnsen)
CHANGES IN VERSION 1.31
-----------------------
BUG FIXES
o (v.1.31.3) pileup() examples require min_base_quality =
10. See https://support.bioconductor.org/p/105515/#105553
CHANGES IN VERSION 1.27
-----------------------
BUG FIXES
o qnameSuffixStart<-(), qnamePrefixEnd<-() accept 'NA' (bug report
from Peter Hickey).
o scanBam() accepts a single tag mixing 'Z' and 'A' format. See
https://support.bioconductor.org/p/94553/
CHANGES IN VERSION 1.25
-----------------------
NEW FEATURES
o *File and *FileList (e.g., TabixFile, TabixFileList)
constructors support NA as 'index'.
o *File and *FileList have accessor method for index.
o asBam(), asSam() provide default desinations.
o idxstatsBam() quickly summarizes the number of mapped and
unmapped reads on each sequence in a BAM file.
SIGNIFICANT USER-VISIBLE CHANGES
o index() by default returns NA rather than character(), but can be
controled with asNA argument.
BUG FIXES
o TabixFileList(TabixFile()) works.
o *File constructors now check that the file argument is length 1,
and that the index argument is length 0 or 1.
CHANGES IN VERSION 1.23
-----------------------
NEW FEATURES
o filterBam can filter one source file into multiple destinations
by providing a vector of destination files and a list of
FilterRules.
o phred2ASCIIOffset() helps translate PHRED encodings (integer or
character) to ASCII offsets for use in pileup()
BUG FIXES
o scanBam() fails early when param seqlevels not present in file.
o Rsamtools.mk for Windows avoids spaces in file paths
CHANGES IN VERSION 1.21
-----------------------
SIGNIFICANT USER-VISIBLE CHANGES
o pileup adds query_bins arg to give strand-sensitive cycle bin
behavior; cycle_bins renamed left_bins; negative values allowed
(including -Inf) to specify bins based on distance from
end-of-read.
o mapqFilter allows specification of a mapping quality filter
threshold
o PileupParam() now correctly follows samtools with
min_base_quality=13, min_map_quality=0 (previously, values were
assigned as 0 and 13, respectively)
o Support parsing 'B' tags in bam file headers.
BUG FIXES
o segfault on range iteration introduced 1.19.35, fixed in 1.21.1
o BamViews parallel evaluation with BatchJobs back-end requires
named arguments
CHANGES IN VERSION 1.19
-----------------------
SIGNIFICANT USER-VISIBLE CHANGES
o FaFile accepts a distinct index file
o Support for cigars > 32767 characters
o Mate pairs use pos and mpos values calculated modulo target
length for pairing, facilitating some representations of mates
on circular chromosomes.
o scanBam no longer translates mapq '255' to 'NA'
BUG FIXES
o segfault on file iteration, introduced in 1.19.35, fixed in
1.19.44
o scanBam correctly parses '=' and 'X'
CHANGES IN VERSION 1.17.0
-------------------------
NEW FEATURES
o pileup visits entire file if no 'which' argument specified for
'ScanBamParam' parameter of pileup. Buffered functionality with
'yieldSize' available to manage memory consumption when working
with large BAM files
o pileup 'read_pos_breaks' parameter renamed to 'cycle_bins':
cycle_bins allows users to differentiate pileup counts based on
user-defined regions within a read.
o pileup uses PileupParam and ScanBamParam instances to calculate
pileup statistics for a BAM file; returns a data.frame with
columns summarizing information extracted from alignments
overlapping each genomic position
o scanBam,BamSampler-method returns requested and actual
yieldSize, and total reads
o seqinfo,BamFileList-method returns the merged seqinfo of each
BamFile; seqlevels and seqlengths behave similarly.
o scanBamHeader accepts a 'what' argument to control input of the
targets and / or text portion of the header, and is much faster
for BAM files with many rnames.
SIGNIFICANT USER-VISIBLE CHANGES
o rename PileupParam class and constructor -> ApplyPileupsParam
o seqinfo,BamFile-method orders levels as they occur in the file,
reverting a change introduced in Rsamtools version 1.15.28
(version 1.17.16).
BUG FIXES
o scanBam(BamSampler(), param=param) with a 'which' argument no
longer mangles element names, and respects yield size
o applyPileups checks that seqlevels are identical across files
o scanFa documentation incorrectly indicated that end coordinates
beyond the range of the sequence would be truncated; they are an
error.
o applyPileups would fail on cigars with insertion followed by
reference skip, e.g., 2I1024N98M (bug report of Dan Gatti).
CHANGES IN VERSION 1.15.0
-------------------------
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)