1.0dev.8: Add -hdp switch to do Hadoop-style error reporting and a progress counter
1.0dev.9: Fix various bugs for stdin reading of non-FASTQ, plus some writes that went to stdout when they shouldn't have
Merge remote-tracking branch 'origin/dev' into hdfs.
Note, since the VCXPROJ files don't merge, this is the dev version;
this won't compile under Windows until I get a chance to use visual studio
to generate new files.

Conflicts:
	SNAPLib/Genome.cpp
	SNAPLib/GenomeIndex.cpp
	SNAPLib/HashTable.cpp
	SNAPLib/SNAPLib.vcxproj
	SNAPLib/SNAPLib.vcxproj.filters