Merge branch 'master' into adina
added fastq iter to ThreadedSequenceProcessor
added support for weird dray fastq format
fixed sodd stuff once and for all
made filter-sodd equivalent to split-fasta-on-circum3
made running split-fasta-on-circum3 more like filter-sodd
tests for sodd filtering
adding contig-coverage script
added printout at end of ThreadedSequenceProcessor
added density explosion filtering script
revise density explosion script to look at more local neighborhoods
added scaffolding option
convenience script for part+extract groups/dist
reformatted MSB2 file appropriately, + script
fixed problem with full paths retained for groupfile prefix
added is_single_partition fn to SubsetPartition
use new is_single_partition fn to validate .part files
hacky-fix to broken tagging problem, maybe?
refactored Makefile for .so/.dylib foo
added _get/_set_tag_density functions ot hashbits