Initial commit - works
minor changes - still doesn't compile here
extracted relevant part of libdeweylab

extracted relevant part of libdeweylab and converted it to a header-only
library.
Added a psl.hh file for PSL-format alignments.

Also updated the Alignment concept, which required making many minor
changes elsewhere.
Fixed Pairset concept and added smart_pairset.

Fixed Pairset concept (and corresponding Mask concept) so that alignment
segments with exceptions are added correctly. Added smart_pairset realization
of the Pairset concept, which is much faster, and has much lower memory usage,
for typical psl alignments.
Fixed TPM reading bug.
Made changes to facilitate testing.
Split up summarize.cpp to facilitate testing.

Moved everything but main from summarize.cpp to summarize_meat.cpp.
Added tests for reading/filtering and stats.
Changed notation: "n choose 2" to "(n+1) choose 2".

(No change in functionality.)
Added new tests to "make test"
Corrected pairset concept and implementation.
Added further tests for prec/recall/F1 computation
Extracted misc stuff to util.hh.
Added kmer summarize program, based on old code.
Moved back some stuff from util.
Improved makefile cross-platform.
Better cross-platform Makefile
Only compute relevant kmer statistics.
Fix bug (with reverse intervals) in mask.