edited raise statements.

added max_intron and code to screen out introns that too large or too small.
lowercased some non-constant variables.
modified all tests based on changes in gimme.py.
removed unused variables.
updated SHA.
adjusted coordinate of splice junctions to start and end of the corresponding intron.
fixed the error that write acceptor seq to the wrong file.
renamed countGenes.py to count_genes.py
renamed sizeSelect.py to size_select.py
added split_sam.py to utils.
added a prfix to output files.
changed output from BAM to SAM
fixed a bug that ignore reads mapped without mates.
changed hard-coded number of nucleotides on each side to SEQLEN variable.

assign SEQLEN to 21
added get_junction_seq() to obtain a sequence of a junction + some flanking nucleotides.
added modified assembly-diff-2.py
add count_spliced_reads2.py
fixed a bug in calculating a wrong exon size.
fixed error in striping BAM suffix.
Merge branch 'master' of github.com:likit/gimme