v0.1.4 refactor core and new features

[timothymillar]

Substantial changes to code base in order to accommodate new features. Command-line-tool names and arguments have changed - see the documentation. Core clustering algorithms are unchanged and will identify the same clusters/features as before.

• Renamed tools
  • remove tef wrapper as it is likely to have a name collision with something
  • tef fingerprint/compare are combined into single tool tefingerprint #63
  • tef preprocess is now tef-extract-informative
  • tef filter-gff is now tef-filter-gff (note: this tools behavior has changes substantially to handle the new gff output)
• Refactored modules
  • core sub-module loci.py re-written to be more flexible #82
  • single data structure for for representing collections of loci
  • arbitrary string length limit removed (use of python string in place numpy strings)
  • split tool logic into separate sub-module fingerprint/py
• New Features
  • tefingerprint
  • trim buffered clusters to extent of read tips
  • count n most common elements per sample in each bin #63 #81
  • use gff annotation for tagging known elements #80
  • join paired clusters using gff annotation #78
  • output files (gff, csv) are optionally pipe-able
  • output files (gff, csv) contain more detailed data
  • can read(anotation gff)/write files compressed with gzip or bz2 #86
  • escape special characters in gff files with percent encodings
  • tef-filter-gff
  • changed to handle new gff output #84
  • use of --any and --all contexts for combining filters
  • unix style wild cards for matching multiple fields
  • read and write gz abd bz2 compressed files #86
  • escape special characters with percent encodings
  • read gff from standard in