v0.6.7

Initial dump of exonerate source, starting at version 0.6.7.

0.6.6 -> 0.6.7
o Fixed memory leak with SListSet
o Simplification of Portal/Span system
o Added short help (-h) command line synopsis
o Implemented C4 model inheritance
o Separated Intron model from est2genome code
o Added --wordhoodjump for large query inputs
o Added --showquerygff and --showtargetgff for GFF dumping
o Added --scanquery option and removed symmetric models

0.6.5 -> 0.6.6
o Fixed bug with nascent HSPs
o Added --verbose option
o Added initial support for dna2protein and protein2dna models
o Renamed GenomicNER -> NER, allowed proteins alignments
o Added --showvulgar --ryo output options
o Fixed wordhood bug when Xs are present in nucleotide sequence
o Added Dynamite-style alignment labels
o Replaced model-specific alignment drawing code
with a single label-based implementation
o Fixed bugs with bootstrapper looking for (unnecessary) region
finding DP implementations for global models
o Added ungapped models - made ungapped model the default

0.6.4 -> 0.6.5
o Added support for 2D spans
o Added support for genomic NER model
o Added basic speedups to Heuristic_Span_integrate
o Fixed bug with query multiplexing
o Added descriptions to alignment output
o Added softmasking support for query or target
o Added thresholds to Optimal_find_path (speed up)
o Added lots more command line options
o Updated man pages, added examples

0.6.3 -> 0.6.4
o Added ability to align sequences exhaustively (slow)
o Major refactoring of all Optimal DP code
o Added Hughey-style reduced space DP implementation
(consisting of region finding, checkpoint finding,
continuation DP and associated tracebacks)
o Fixed more bugs with splice site prediction and gtag_only
o Fixed more bugs with non-diagonal HSPs
o Fixed bug with derived model creation
o Fixed several bugs with terminal matrix upper bound calculation
and end HSP component integration
o Added many more command line options and updated man page

0.6.2 -> 0.6.3
o Added bootstrapping system for static linking of c4 models
o Added support for est2genome model
o Fixed bugs with est2genome model and splice site prediction
o Started module-localised command-line arguments
o Added C4_Model_configure_extra to supply C4_Model
with {init,exit}_{func,macro} like C4_Calc
o Updated man page (still incomplete)

0.6.1 -> 0.6.2
o Added hub directory (and moved UGAM to it)
o Added GAM: Gapped Alignment Manager
o Added Analysis: High-level analysis object
o Added program directory and exonerate program
o Moved sequence_type from FastaDB to Sequence
o Moved BSDP threshold from Heuristic -> HPair
o Various other small fixes

0.6.0 -> 0.6.1
o Added FastaDB_Seq_revcomp()
o Many minor bugs fixed (mostly found by valgrind)
o Simplified FSM memory management to use glib memchunks
(previous implemention was slower and buggy)
o Added SList: Efficient Single-linked Lists
o Many fixes for non-diagonal HSPs
o Added UGAM: UnGapped Alignment Manager

0.5.0 -> 0.6.0
o Changed from ensembl-nci code base to exonerate
o Removal of NCI
o Major refactoring including many minor changes not listed here
o Build system now builds statically when using gprof
o Build system now supports gcov coverage analysis
o Build system supports "make check" to run tests
(a lot more of the tests do something worthwhile now)
o Started a man page for exonerate. RTFM!
o FastaDB object changed to inherit from Sequence
o Sequence object includes strand information
o Rewrite of word neighbourhood generation using a new algorithm,
- now much faster and without memory overhead
o Allowed word neighbourhood generation by dropoff
o Added support for non-diagonal HSPsets
o Changed plugin system to recognise out-of-date modules
o Changed plugin system to support multi-architecture farms
o Added underflow/overflow protection to DP implementations
o Used Region object much more to simplify C4
o Changes to flow of control around C4<->HSP interfaces
o Added exit_func and exit_macro to C4_Calc
o Simplified splice site prediction coordinate system
o Converted est2genome model to use PSSM splice site prediction
o Fixed C4_Model_select() to avoid copying redundant calcs