CHANGES IN VERSION 1.11.*
-------------------------

BUG FIXES

    o completely free razip, bgzip files when done

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)
