Putting in place template functions for processing outgroup genomes.
Adding some notes for how we might implement the coverage filtering.
Add coverage + trimSequences utils
Fix bug on merging blocks
Add tests for trim utility/fix a few bugs
iterative outgroups working-ish in cactus_blast

(need tests)
fix cigar sort
Speed up trimSequences
Add multiple outgroups test
Change to array-based method for coverage and update tests
More fiddling with coverage/overlap diagnostics

(chimp coverage doesn't work because there are spaces in the header)
Make cactus_coverage fail on duplicate FASTA header

and remove chimp from test, since its headers aren't unique
Accumulate outgroup fragments
Allow multiple outgroups

(no xml option yet)
Config option for multiple outgroups (and change default)
Make one trimmed fa for each outgroup instead of one for all fragments
Add test comparing aligning all outgroups vs trimming strategy
Multiple-outgroups pipeline integration almost working

Major issues:
- caf crashes on reading converted alignments file
  (seq Names probably not written correctly)
- experiment XML still modified
- no filtering by identity
Change from using sequence names to cap names

Caf phase still fails but finds the pinch threads this time.
Also, filtering by identity is fixed.
Use 1-based coordinates when converting alignments