abyss-fac: Include NG50 statistics.

* DataLayer/fac.cc (opt): New option, --exp-size, return the n:NG50 and NG50 given the
expected genome size.
(printContiguityStatistics): Include NG50 and n:NG50 headings.
* Common/Histogram.h (argMin): Factored from weightedPercentile.
(printContiguityStats): Calculate and print NG50 and n:NG50.
abyss-fac: Add option to count ambiguity codes

* DataLayer/fac.cc (opt): New option, --count-ambig, to count ambiguity
codes in sequences.
(printContiguityStatistics): Count full sequence length if count-ambig
specified.
ignore tags file used with ctags
Make popcnt portable
Fix compiler error for non-GNU compilers
Remove popcnt options from configure
abyss-map: Force output order to the same as input.

* Map/map.cc (find): Wait for the current alignment to be at the
front of g_pq.
(find): Push the read ID's into g_pq as the reads are read.
abyss-map: new option --order to order output.
Replace baseToCode switch with lookup table.
abyss-filtergraph: New option --remove to remove contigs from graph.
MPICH: Link against -lmpl
AdjIO: Bug fix for non-GCC compilers
PopBubbles: Fix error related to dialign.

* PopBubbles/PopBubbles.cpp (alignMulti): Use alignGlobal instead of
dialign.
abyss-fixmate: Write physical coverage to wiggle file.

ParseAligns/abyss-fixmate.cc (main): New option -c to specify wiggle
file for physical coverage output.
(handlePair): Increment coverage at locations inside a paired mapping.
(printCov): Print the coverage to the wiggle file.
(parseTag): Parse headers to reserve the correct size in the coverage
vectors.
Produce call graphs and inheritance graphs with doxygen
abyss-fixmate: Report error when all reads are mateless.
abyss-fixmate: Improve FF orientation error.
Updated and improved README documentation
Correct spelling of GitHub.
Fix autoconf and automake links.