Added --keep_tmpfiles option to deepseq_alignment_wrapper.py; test fix.

Simple --keep_tmpfiles command-line option to keep the raw alignment sam
files for debugging purposes.

Changed run-test reference files to not assume the bowtie version is
0.*, because I updated to 1.0.0 (the earlier one had a bug with read
names sometimes getting truncated on spaces and sometimes not!)
Rewrote to take much less memory!

Instead of reading the whole genome-alignment and cassette-alignment
files into memory at once in order to compare how reads align against
both cases, I wrote a two-file generator that goes over both files in
parallel and returns the joint results for each read.  Also had to
refactor the rest

New functions:
 - aln_generator_from_single_samfile and
   aln_generator_from_two_samfiles_parallel replace
   make_aln_dict_from_samfile
 - reduce_alignment_list replaces reduce_alignment_dict;
   prioritize_cassette_reads changes in place (very simple change in
   both cases, just changed them from acting on whole dictionary to a
   single list)
 - categorize_reads_print_to_files also changes in place (similar simple
   change; it now takes category_readcounts as an argument to modify,
   instead of generating it fully in one run; also returns category now,
   just in case I want to use that later)
 - main function refactored to make all that work

After some debugging, all run-tests pass!
More informative and shorter message for multiple cassette alignments.