remove `createSubfeatures` switch from BAM stores, just have it always on.  the subfeatures are lazily created anyway.
make SNPCoverage pay attention to skipped regions in alignments. fixes #274
add newline to "not capable" die message in ucsc-to-json
add `mismatchScale` conf var to SNPCoverage tracks
fix snpcoverage value display sometimes reporting NaN%
Wiggle error handling bugfix
avoid repeated "."s in too-many-features messages
actually, skipped regions should count toward coverage, but be displayed as a mismatch
display strand counts in SNPCoverage for reference reads
add Pod::Usage to new-plugin.pl
stop moving src/dojo/nls to src/nls in the build
fix trailing comma
Merge remote-tracking branch: upstream/master