added *.count.summary file to count.groups command. added deltaq and insert parameter...

added *.count.summary file to count.groups command. added deltaq and insert parameters to make.contigs and changed contigs.report file. added illumina1.8+ format to fast commands. added contigsreport, align report and summary files to screen.seqs to allow files to be screened using their inputs.  added minoverlap, ostart, oend, mismatches, maxn, minscore,maxinsert, minsim parameters to screen.seqs. added optimization types of minoverlap, ostart, oend, mismatches, maxn, minscore,maxinsert, minsim to screen.seqs.  added getNumNs function to sequence class. working on Windows \\ issue.