Alpha-0.1.4

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