CHANGES IN VERSION 2.16.0
-------------------------

NEW FEATURES

    o exonAlignDepth, exonLoessModel, geneAlignDepth classes added
    o saveAldData, cutFlatAlignDepth, junctionSites, getNormFactor
		functions added


SIGNIFICANT USER-VISIBLE CHANGES

    o (none)

BUG FIXES

    o (none)


CHANGES IN VERSION 2.13.0
-------------------------

NEW FEATURES

    o sampleBamFiles and samplesAlignDepth classes added


SIGNIFICANT USER-VISIBLE CHANGES

    o (none)

BUG FIXES

    o Corrected [extern "C" ] position in rbamtools.h

CHANGES IN VERSION 2.13.0
-------------------------

NEW FEATURES

    o (none)


SIGNIFICANT USER-VISIBLE CHANGES

    o (none)

BUG FIXES

    o Corrected [extern "C" ] position in rbamtools.h


CHANGES IN VERSION 2.12.0
-------------------------

NEW FEATURES

    o extractBamRegions

    o rangeSegCount class


SIGNIFICANT USER-VISIBLE CHANGES

    o The functions reader2fastq and range2fastq will be deprecated soon and
	replaced by readerToFastq and rangeToFastq

BUG FIXES

    o Corrected bug in gapSiteList.h which caused crashes in multiply repeated merges

    o Changed Variable type from Integer to unsigned long long int in
	C functions where alignment numbers are carried.

    o Corrected a PROTECT / UNPROTECT imbalance which showed up incidentally.



CHANGES IN VERSION 2.10.0
-------------------------

NEW FEATURES

    o Added support for Description (DS) segment in header program

    o Added support for Supplementary Alignment (0x800) segment in alignment FLAG


SIGNIFICANT USER-VISIBLE CHANGES

    o The functions create.index, load.index and create.idx.batch will
	be deprecated soon and replaced by createIndex, loadIndex and
	createIdxBatch.

BUG FIXES

    o Fixed erroneous FLAG re-setting algorithm

    o Enclosed range2fastq example in "\dontrun{}" in order to avoid
	checking errors (File could not be opened) on OSX snowleopard

    o Replaced rand() by runif() in (samtools) ksort.h
	(due to NOTE in devel CRAN win-builder:
		"Compiled code should not call (...) the C RNG")

CHANGES IN VERSION 2.9.14
-------------------------

NEW FEATURES

    o Included this NEWS file and a ChangeLog file

    o Added test directory (tests are executed on R CMD check)


SIGNIFICANT USER-VISIBLE CHANGES

    o Extended plotAlignDepth function: Option for plotting of exon positions added

BUG FIXES

    o (none)
