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## Change Log for package rbamtools
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30.Okt.12	[initialize.gapList] Made printout message optional 
															(verbose)

31.Okt.12	[bamRange] Included test for initialized index

31.Okt.12	Check for open reader in getHeader, getHeaderText, 
															getRefCount

01.Nov.12	[get_const_next_align] added to correct memory leak.

08.Nov.12	Reading and writing big bamRanges (pure C, no R) 
													valgrind checked.

09.Nov.12	[bamCopy.bamReader] Added which allows refwise copying.

31.Dec.12	gapSiteList class added

11.Jan.13	bamGapList class added

06.Feb.13	First successful test of bamGapList on 36 BAM-files
												(871.926 aligns/sec)

20.Feb.13	Fixed Error in merge.bamGapList

27.Feb.13	Renamed createIndex -> create.index and loadIndex
		-> load.index and bamSiteList -> bamGapList

18.Apr.13	Corrected some memory leaks in C-Code as reported
				by Brian Ripley

22.Apr.13	Added (read-) name and revstrand to as.data.frame.bamRange
							(as proposed by Ander Muniategui)

11.Jun.13	Added reader2fastq and range2fastq functions 
							(2.5.3, valgrind tested)

11.Jun.13	Changed signature for bamSave: added refid argument
		(needed to prevent samtools crashes when creating BAM files
		with single align regions and appropriate refSeqDict entries)
		(2.5.4, valgrind tested)

12.Jun.13	Added extractRanges function (2.5.5)

21.Jun.13	Added bamAlign function (2.5.6)

01.Jul.13	Added bamCount function (2.5.8)

02.Jul.13	Added bamCountAll function, valgrind tested (2.5.9)

18.Jul.13	Changed 'nGapAligns' to 'nAlignGaps (2.5.10)
												nGapAligns deprecated!

24.Jul.13	Added alignQual function, valgrind tested (2.5.11)

28.Jul.13	Added alignDepth function, valgrind tested (2.5.12)

13.Aug.13	Added countTextLines function, valgrind tested (2.6.1)

26.Aug.13	Removed "coerce" from Namespace declaration

02.Sep.13	Changed "cat" to "message"

10.Jun.14	On CRAN after correction of "Mis-alignment errors"

19.Jun.14	Re-introduction of changes after resetting to 2.7.0 due to
				internal errors

21.Jul.14	Updated plotAlignDepth: Option for plotting of exon
				positions added (2.9.14)

14.Jul.14	Added test directory

28.Jul.14	Added NEWS and ChangeLog file

29.Sep.14	Added support for DS segment in headerProgram (@PG).
			Added support for Supplementary alignmnet FLAG.
			Corrected error in resetting FLAG values.
			(2.9.16)

29.Sep.14	Replaced rand() by runif() in ksort.h
			Enclosed range2fasta, reader2fastq examples in \dontrun{}
			(File could not be opened error on OSX snowleopard)

30.Sep.14	Prepared depreciation of create.index, load.index,
										create.idx.batch
			which will be replaced by createIndex, loadIndex and 
										createIdxBatch (2.10.0)

03.Nov.14	Changed nAligns data type to unsigned long long int (2.10.2)

05.Nov.14	Corrected error in gapSiteList.h which caused 
					"free(): invalid next size (fast)" error

25.Nov.14	Added rangeSegCount class.

01.Feb.16   	Corrected extern "C" problem in rbamtools.h

23.May.16	New Framework for counting align depth on multiple BAM 
				files added:
					sampleBamFiles class, 
					exonAlignDepth, exonLoessModel and geneAlignDepth 
						classes
					saveAldData, cutFlatAlignDepth, junctionSites, 
						getNormFactor functions added

12.Oct.16	Renamed *.r files to *.R

18.Mar.17	Changed test files due to check error on CRAN
