June 26, 2013 - 1.10.5
(1) Fixed a bug in outputting mapping results for paired-end reads which can not be mapped as a pair.

June 25, 2013 - 1.10.4
(1) Fixed RGUI output problem.

June 21, 2013 - 1.10.3
(1) Major update to featureCounts function.
(2) Incorporated the changes made in Subread 1.3.5 patches 1-4.

April 5, 2013 - 1.10.1
(1) Updated citations.

March 31, 2013 - 1.9.8
(1) Document improvement

March 29, 2013 - 1.9.7
(1) Changes to the configure file and Makevars.Linux
(2) Changes to sorted-hashtable.c

March 28, 2013 - 1.9.6
(1) Fix the multithreading issue
(2) Documentation improvements

March 27, 2013 - 1.9.5
(1) Updated CITATION file.
(2) Updated documentation.
(3) Modified the arguments of featureCounts() function
(4) featureCounts() function now accepts BAM files as input.

March 14, 2013 - 1.9.3
(1) Mac support was added.
(2) Subread version 1.3.1 was used.
(3) Fix warnings related to C functions.

August 24, 2012 - 1.7.7
(1) Align and subjunc functions are now updated using the latest Subread package (1.3.0 on sourceforge.net).
(2) Major updates to SNP calling function and the function for removing duplicated reads.

August 23, 2012
(1) Temporary files generated by functions will be temporarily stored in the current working directory.

June 30, 2012 
(1) Add mm10 annotation file to featureCounts function. 

June 26, 2012 - 1.7.6
(1) Add an option to featureCounts to count fragments for paired-end sequencing data.
(2) Disable the running of example included in createAnnotationFile.Rd.

June 14, 2012 - 1.7.5
(1) featureCounts function now accepts a data frame as the annotation input.

June 8, 2012 - 1.7.4
(1) Change static memory allocation to dynamic memory requests for a number of functions to reduce memory use when the package is loaded.
(2) The buildindex function no longer requies an allocation of 1GB continous memory block.

May 31, 2012 - 1.7.3
(1) Tim Triche added createAnnotationFile function to convert annotations to the format which can be used by featureCounts.

April 27, 2012 - 1.7.2
(1) Bug fix to incorrect CIGAR strings.

April 3, 2012 - 1.7.1
(1) Bug fix to parameter passing from R to C for align and subjunc
(2) Fix memory leakage for align and subjun.

March 26, 2012 - 1.5.8
(1) Bug fixes to align and callSNPs function.

March 22, 2012 - 1.5.7
(1) Major updates to align and subjunc functions.

March 21, 2012 - 1.5.6
(1) Add snpCalls function.
(2) Add removeDupReads function.

Feb 15, 2012 - 1.5.5
(1) Bug fix to subjunc parameters passed to the underlying C program.

February 14, 2012 - 1.5.4
(1) Fixed the bug of mapping reads out of chromosome boundary.

Junuary 17, 2012 - 1.5.3
(1) Align function can now report uniquely mapped reads only.
(2) Buildindex function now includes the reference sequences in the built index by default.
(3) Subjunc now supports up to 16bp INDELs.
(4) Subjunc supports extra splicing donor/receptor sites (GC-AG and GT-AT), in addition to the canonical one(GT-AG).

November 7, 2011 - 1.5.2
(1) Bug fix to chr3 length issue.

November 2, 2011 - 1.5.1
(1) Bug fix to the flag field in SAM output 

September 28, 2011 - 1.2.1
(1) propmapped function now returns a data frame.
(2) remove file name restraint in detectionCall function.
(3) output of featureCounts function was changed to a list.
(4) fixed the incorrect use of ppois function in detectionCall function

August 30, 2011 - 1.2.0
(1) Add subjunc function which can be used to find exon junctions.
(2) Add functions for determining detection p values for each gene in RNA-seq data.

July 26, 2011 - 1.1.1
featureCounts function now supports human data and allows users to provide their annotation data.

July 22, 2011 - 1.1.0
Add featureCounts function, which counts number of mapped reads for each feature.

1.0.0
Package release.
