little alignment improved

bug with paired end fixed.

improvements in alignment accuracy

Minor fixes

Minor fix in BWT index generation

Minor fix in BAM file generation.

Included automatic detection of the number of chromosomes of the reference genome (therefore, option --max-num-chromosomes has been deleted).

Included a new option (--max-num-chromosomes) in order to set the number of chromosomes of the reference genome ( by default 24, human genome (1-22,X,Y).

Paired-end mode implemented.

Fixed a minor bug in the BAM file generation