resolved issue 18 + other small changes

The following changes have been made:

1. Issue 18 resolved - FASTQ parsing of reads and output alignments which caused a segmentation fault
2. resolved Valgrind memory leaks for sliding window intervals & incrementing the s_align* array pointer 
3. -m option edited to accept scientific notation values, though rounded to the nearest int (input is in Mbytes)
4. few small changes to _autotools_batch_.sh & the option menu