NEWS

Rsamtools 2.16

NEW FEATURES

(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)

Rsamtools 2.10

DEPRECATED AND DEFUNCT

(v 2.9.1) Deprecate applyPileups() in favor of pileup().

Rsamtools 2.8

NEW FEATURES

(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.

Rsamtools 2.4

BUG FIXES

(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.
(v 2.3.5) Fix regression introduced by v 2.3.2

NEW FEATURES

(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)

Rsamtools 2.0

SIGNIFICANT USER-VISIBLE CHANGES

Migrate Rsamtools to Rhtslib. See Rsamtools/migration_notes.md for more information about this migration.
Remove unused fields from BamRangeIterator
Remove BAM header hash init for pileup (already memoized in Rhtslib)

Rsamtools 1.34

BUG FIXES

(v 1.34.1) indexFa,FaFile-method correctly updates the index path.

Rsamtools 1.33

NEW FEATURES

(v 1.33.4, 1.33.7) scanBamFlag() gains isSupplementaryAlignment support.

BUG FIXES

(v 1.33.1) Do not try to grow NULL (not-yet-encountered) tags (https://support.bioconductor.org/p/110609/ ; Robert Bradley)
(v 1.33.5) Check for corrupt index (https://github.com/Bioconductor/Rsamtools/issues/3 ; kjohnsen)

Rsamtools 1.31

BUG FIXES

(v.1.31.3) pileup() examples require min_base_quality = 10. See https://support.bioconductor.org/p/105515/#105553

Rsamtools 1.27

BUG FIXES

qnameSuffixStart<-(), qnamePrefixEnd<-() accept 'NA' (bug report from Peter Hickey).
scanBam() accepts a single tag mixing 'Z' and 'A' format. See https://support.bioconductor.org/p/94553/

Rsamtools 1.25

NEW FEATURES

*File and *FileList (e.g., TabixFile, TabixFileList) constructors support NA as 'index'.
*File and *FileList have accessor method for index.
asBam(), asSam() provide default desinations.
idxstatsBam() quickly summarizes the number of mapped and unmapped reads on each sequence in a BAM file.

SIGNIFICANT USER-VISIBLE CHANGES

index() by default returns NA rather than character(), but can be controled with asNA argument.

BUG FIXES

TabixFileList(TabixFile()) works.
*File constructors now check that the file argument is length 1, and that the index argument is length 0 or 1.

Rsamtools 1.23

NEW FEATURES

filterBam can filter one source file into multiple destinations by providing a vector of destination files and a list of FilterRules.
phred2ASCIIOffset() helps translate PHRED encodings (integer or character) to ASCII offsets for use in pileup()

BUG FIXES

scanBam() fails early when param seqlevels not present in file.
Rsamtools.mk for Windows avoids spaces in file paths

Rsamtools 1.21

SIGNIFICANT USER-VISIBLE CHANGES

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.
mapqFilter allows specification of a mapping quality filter threshold
PileupParam() now correctly follows samtools with min_base_quality=13, min_map_quality=0 (previously, values were assigned as 0 and 13, respectively)
Support parsing 'B' tags in bam file headers.

BUG FIXES

segfault on range iteration introduced 1.19.35, fixed in 1.21.1
BamViews parallel evaluation with BatchJobs back-end requires named arguments

Rsamtools 1.19

SIGNIFICANT USER-VISIBLE CHANGES

FaFile accepts a distinct index file
Support for cigars > 32767 characters
Mate pairs use pos and mpos values calculated modulo target length for pairing, facilitating some representations of mates on circular chromosomes.
scanBam no longer translates mapq '255' to 'NA'

BUG FIXES

segfault on file iteration, introduced in 1.19.35, fixed in 1.19.44
scanBam correctly parses '=' and 'X'

Rsamtools 1.17.0

NEW FEATURES

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
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.
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
scanBam,BamSampler-method returns requested and actual yieldSize, and total reads
seqinfo,BamFileList-method returns the merged seqinfo of each BamFile; seqlevels and seqlengths behave similarly.
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

rename PileupParam class and constructor -> ApplyPileupsParam
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

scanBam(BamSampler(), param=param) with a 'which' argument no longer mangles element names, and respects yield size
applyPileups checks that seqlevels are identical across files
scanFa documentation incorrectly indicated that end coordinates beyond the range of the sequence would be truncated; they are an error.
applyPileups would fail on cigars with insertion followed by reference skip, e.g., 2I1024N98M (bug report of Dan Gatti).

Rsamtools 1.15.0

NEW FEATURES

asSam converts BAM files to SAM files
razip, bgzip re-compress directly from .gz files
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

bgzip default extension changed to '.bgz'
seqinfo,BamFile-method attempts to return seqnames in 'natural' order, e.g., chr1, chr2, ...
yieldSize now works on BAM files queried with ranges. Successive ranges are input until the total number of records first equals or exceeds yieldSize..
scanFa supports DNA, RNA, and AAStringSet return objects

BUG FIXES

scanFa returns correct sequence at the very end of files
razip compresses small files
applyPileups no longer crashes in the absence of an index file

Rsamtools 1.14.0

NEW FEATURES

seqinfo(FaFile) returns available information on sequences and lengths on Fa (indexed fasta) files.
filterBam accepts FilterRules call-backs for arbitrary filtering.
add isIncomplete,BamFile-method to test for end-of-file
add count.mapped.reads to summarizeOverlaps,*,BamFileList-method; set to TRUE to collect read and nucleotide counts via countBam.
add summarizeOverlaps,*,character-method to count simple file paths
add sequenceLayer() and stackStringsFromBam()
add 'with.which_label' arg to readGAlignmentsFromBam(), readGappedReadsFromBam(), readGAlignmentPairsFromBam(), and readGAlignmentsListFromBam()

SIGNIFICANT USER-VISIBLE CHANGES

rename: readBamGappedAlignments() -> readGAlignmentsFromBam() readBamGappedReads() -> readGappedReadsFromBam() readBamGappedAlignmentPairs() -> readGAlignmentPairsFromBam() readBamGAlignmentsList() -> readGAlignmentsListFromBam() makeGappedAlignmentPairs() -> makeGAlignmentPairs()
speedup findMateAlignment()

DEPRECATED AND DEFUNCT

deprecate readBamGappedAlignments(), readBamGappedReads(), readBamGappedAlignmentPairs(), readBamGAlignmentsList(), and makeGappedAlignmentPairs()

BUG FIXES

scanVcfHeader tolerates records without ID fields, and with fields named similar to ID.
close razip files only once.
report tabix input errors

Rsamtools 1.12.0

NEW FEATURES

BamSampler draws a random sample from BAM file records, obeying any restriction by ScanBamParam().
Add argument 'obeyQname' to BamFile. Used with qname-sorted Bam files only.
Add readBamGAlignmentsList function for reading qname-sorted Bam files into a GAlignmentsList object.

USER-VISIBLE CHANGES

bamPath and bamIndicies applied to BamViews returns named vectors.
'yieldSize' argument in BamFile represents the number of unique qnames when 'obeyQname=TRUE'.

BUG FIXES

completely free razip, bgzip files when done.
sortBam, indexBam fail gracefully on non-BAM input.
headerTabix on an open TabixFile no longer reads the first record
scanBcfHeader provides informative error message when header line ('#CHROM POS ...') is missing

Rsamtools 1.10.0

NEW FEATURES

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.
Add getDumpedAlignments(), countDumpedAlignments(), and flushDumpedAlignments() low-level utilities for manipulating alignments dumped by findMateAlignment().
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

scanBamFlag isValidVendorRead deprecated in favor of isNotPassingQualityControls
Rename makeGappedAlignmentPairs() arg 'keep.colnames' -> 'use.mcols'.

BUG FIXES

close razip, bgzip files when done
bamReverseComplement<- failed to return the updated object
scanBcfHeader works on remote files
allow asBam to work without warnings on header-only SAM files
some bug fixes and and small performance improvements to findMateAlignment()
fix bug in readBamGappedAlignmentPairs() where fields and tags specified by the user were not propagated to the returned GappedAlignmentPairs object

Rsamtools 1.8.0

NEW FEATURES

Add readBamGappedAlignmentPairs() (plus related utilities findMateAlignment() and makeGappedAlignmentPairs()) to read a BAM file into a GappedAlignmentPairs object.

SIGNIFICANT USER-VISIBLE CHANGES

update samtools to github commit dc27682f70713a70d4f31bca652cf78e00757da2
Add 'bitnames' arg to bamFlagAsBitMatrix() utility.
By default readBamGappedAlignments() and readBamGappedReads() don't drop PCR or optical duplicates anymore.

BUG FIXES

readBamGappedAlignments handles empty 'tag' fields
scanTabix would omit variants overlapping range ends
scanFa would segfault on empty files or empty ids

Rsamtools 1.6.0

NEW FEATURES

TabixFile, indexTabix, scanTabix, yieldTabix index (sorted, compressed) and parse tabix-indexed files
readBamGappedReads(), bamFlagAsBitMatrix(), bamFlagAND()
Add use.names and param args to readBamGappedAlignments(); dropped which and ... args.
PileupFiles, PileupParam, applyPileup for visiting several BAM files and calculating pile-ups on each.
Provide a zlib for Windows, as R does not currently do this
BamFileList, BcfFileList, TabixFileList, FaFileList clases extend IRanges::SimpleList, for managings lists of file references
razfFa creates random access compressed fasta files.
count and scanBam support input of larger numbers of records; countBam nucleotide count is now numeric() and subject to rounding error when large.
Update to samtools 0.1.17
asBcf and indexBcf coerces VCF files to BCF, and indexes BCF
Update to samtools 0.1.18
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

ScanBamParam argument 'what' defaults to character(0) (nothing) rather than scanBamWhat() (everything)
bamFlag returns a user-friendly description of flags by default

BUG FIXES

scanBam (and readBamGappedAlignments) called with an invalid or character(0) index no longer segfaults.
scanBcfHeader parses values with embedded commas or =
scanFa fails, rather than returns incorrect sequences, when file is compressed and file positions are not accessed sequentially
scanBcf parses VCF files with no genotype information.
scanBam called with the first range having no reads returned invalid results for subsequent ranges; introduced in svn r57138
scanBamFlag isPrimaryRead changed to isNotPrimaryRead, correctly reflecting the meaning of the flag.

Rsamtools 1.4.0

NEW FEATURES

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.
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.
asBam converts SAM files to (indexed) BAM files
FaFile, indexFa, scanIndexFa, scanFa index and parse (indexed) fasta files.

BUG FIXES

scanBamFlag isValidVendorRead had reversed TRUE/FALSE logic
Attempts to read too many records caught more gracefully.
samtools output to fprintf() or calls to exit() are handled more gracefully

Rsamtools 1.2.0

NEW FEATURES

Update to samtools 0.1.8
Update to samtools svn rev 750 (Mon, 27 Sep 2010)
sortBam sorts a BAM file

BUG FIXES

Attempts to parse non-existent local files now generate an error
Reads whose last nucleotide overlaps the first of a range are now scanned / counted.
scanning / counting reads late in large Windows files is fast
scanBam tag fields of type 'A' parsed correctly

Rsamtools 1.0.0

SIGNIFICANT USER-VISIBLE CHANGES

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
readBamGappedAlignments replaces readBAMasGappedAlignments

NEW FEATURES

ScanBamParam() accepts 'tag' argument for parsing optional fields
BamViews can be used with scanBam, countBam, readBamGappedAlignments

BUG FIXES

No changes classified as 'bug fixes' (package under active development)