CHANGES IN VERSION 1.12.2 ------------------------- BUG FIXES o close razip files only once 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)