New interface for processing regions

[reedacartwright]

Update Region and Contig Interface

• Handle regions in BamPileup instead of Bam::File
  • Create a parser for bed files
  • Support slurping bed files
  • Add ContigIndex class
  • Miscellaneous bug fixes
  • Improve tests

Improve dng-pileup

• Support slurping regions again
• Support filter in number of alleles
• Improve tests

[reedacartwright]

Jenkins, retest this please

[reedacartwright]

Jenkins, retest this please

[codecov[bot]]

Codecov Report

Merging #246 into develop will increase coverage by 0.68%. The diff coverage is 73.59%.

@@             Coverage Diff             @@
##           develop     #246      +/-   ##
===========================================
+ Coverage    71.82%   72.51%   +0.68%     
===========================================
  Files           70       70              
  Lines         6552     6607      +55     
  Branches      1147     1156       +9     
===========================================
+ Hits          4706     4791      +85     
+ Misses        1372     1336      -36     
- Partials       474      480       +6

Impacted Files	Coverage Δ
src/lib/stats.cc	91.83% <100%> (+0.05%)	:arrow_up:
src/include/dng/depths.h	95.86% <100%> (+0.3%)	:arrow_up:
src/include/dng/task/pileup.xmh	100% <100%> (ø)	:arrow_up:
src/lib/task/pileup.cc	58.16% <26.82%> (-2.74%)	:arrow_down:
src/lib/ad.cc	67.87% <38.23%> (+0.21%)	:arrow_up:
src/lib/task/loglike.cc	81.85% <43.47%> (-2.06%)	:arrow_down:
src/include/dng/hts/bam.h	75.29% <55.55%> (+16.96%)	:arrow_up:
src/include/dng/detail/varint.h	89.47% <80%> (-10.53%)	:arrow_down:
src/lib/task/call.cc	82.47% <80.95%> (-0.66%)	:arrow_down:
src/include/dng/io/bcf.h	70.09% <87.5%> (-0.28%)	:arrow_down:
... and 6 more

---

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update ce84763...995ba3d. Read the comment docs.