Mutascope Files

UPDATES:

####   V0.5.6  #######
First official release of Mutascope!

####   v0.5.7  #######
Fixed a small bug with the Read-Group-Bias score

####   v1.0.0  #######
The First FULL release of Mutascope!
Updates include:
	- Now works with new BWA indexing
		 Users can now use any version of BWA
	- All new QC metrics
		a) Alignment statistics
		b) reads per amplicon statistics
		c) variant plot
	- Improved running time
		 The xpileup command implements a new method that reduces the run time from 2 hours to 20 minutes!
	- new strand specific method
		 The strand specific information is now taken directly from the BED file
	- logR ratio for each amplicon
	- Outputs Somatic, Germline and LOH variants based on the genotypes called
	- xpileup files are now stored as .gz files to save on hard-drive space
	- calcErrorRates and callSomatic both take in .xpileup.gz files.
	- User can now specify to use the Tumor sample's Error rate files.
	- The default minimum frequency to call a germline variant is now set to 15%
	- fixed random bugs in the code
		 Bug fixed when clipping primers from BAM files. Used to only work with reads of length 151 now works with reads of any length
		 Bug fixed when calculating the fisher-exact p-value
		 Bug fixed when filtering LOH variants in the VCF file
		
####   v1.0.1  ########
	-fixed bug that was preventing from running multiple instances from the same working directory
	-corrected various typos
 
####   v1.0.2  ########
	-REF and ALT allele at multiallelic indels sites are now indicated following the vcf convention.