CHANGES IN VERSION 2.2 ---------------------- BUG FIXES o (v 2.2.2) Correctly handle '*' ('unknown') RNAME during paired-end processing. See https://github.com/Bioconductor/Rsamtools/issues/16. o (v 2.2.3) Fix regression introduced by v 2.2.2. 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)