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2.3.0 -> 2.4.0
o Fixed many thread safety bugs
o Fixed bugs with large files over 4GB
o Modified client to work with multiple servers
o Fixed server to handle SIGPIPE
o Added support for FOSN input (can be files, directories or servers)
o Fixed bug with --wordambiguity and --wordjump (with normal FSM)
o Added %pS to --ryo (percent self score over equivalenced regions)
2.2.0 -> 2.3.0
o Fixed several bugs with thread safety for exonerate-server
o Fixed bug with custom genetic codes not working
o Fixed bug with overflow of seedrepeat horizon in hspset
o Added passing of wordlimit params to server
o Implemented --cores option for multi-threaded alignment
o Added identity and similarity score for GFF genes and exons
o Increased default FSM memory limit to 256Mb
o Added --revcomp option to disable searching of reverse complement
o Fixed bug with compact-FSM (VFSM) based database searching
o Added --wordambiguity option for searching ambiguous reference seqs
o Fixed bug with esd2esi and .esd files >2Gb
2.1.0 -> 2.2.0
o Fixed bug with esd2esi when softmasking is off
o Removed all GMemChunk usage due to caching problems with glib-2
o Fixed various minor memory leaks
2.0.0 -> 2.1.0
o Fixed portability bugs for x86_64
o Added linecount: tag for long client:server messages
o Added setsockopt(TCP_NODELAY) to improved socket performance
o Changed server to use pthreads by default to avoid LSF memlimit problems
o Added faster implementation of Sequence_strncpy()
o Fixed bug with sequence caching
o Added -V 3 client-server debug code
o Prevented sub-optimial alignments below geneseed threshold from appearing
o Fixed sorting of translated indices
o Completed implementation of server-side geneseed
o Fixed bug with .esd file parsing
o Made compilation use glib2 by default
o Fixed SDP memory management bug
o Fixed segfault bug with --refine (Thanks to Don Gilbert)
o Improved splice site scoring
o Reverted to protein substition scoring for cd2g model
o Fixed bug with fasta parser and \r\n type newlines
1.4.0 -> 2.0.0
o Modified exonerate to work in Client:Server mode
o Fixed --refine to work with SDP alignments
o Disabled codegen warnings from bootstrapper during compilation
o Added --geneticcode option for using alternative genetic codes
o Added --splice5 and --splice3 to allow alternative splice site PSSMs
o Fixed several bugs when scanning query sequences (eg. --forcescan query)
o Fixed to report query on forward strand whenever possible.
o Fixed --ryo sequence dumping with --bestn
o Fixed a bug with missing seeds when using --annotation
o Changed license to GPLv3
o Added protein2dna:bestfit and protein2genome:bestfit models
(works with exhaustive alignment only)
1.3.0 -> 1.4.0
o Improved splice site cache memory management
o Added --geneseed option to speed up large-scale analysis
o Fixed a bug with 3'utr coordinates in GFF output
o Fixed a crash during GFF dumping when using glib2
o Added error message for failed seeks when input is stdin
1.2.0 -> 1.3.0
o Fixed a bad memory leak in boundary.c
o Fixed bug with selenocysteines in query sequences
o Fixed bug with subsequence creation (and --ryo problems)
o Fixed a bug with transition mapping in reduced space alignments
o Removed variable_submat to fix bugs with codegen and allow speed ups
o Fixed bug with --usetlaaa and translated models
o Fixed emit calculation in HPair for BSDP
o Added C field to vulgar for disambiguation of codon matches
o Fixed bug with region finding in exhaustive DP codegen
o Fixed GFF bugs (start always < end) and off-by-one bug on rev strand
o Fixed bugs with codegen for cd2g
o Fixed bug with chained silent transitions in reduced space traceback
o Fixed bug broken bigseq comparisons
o Fixed --percent and --bestn ungapped comparisons
1.1.0 -> 1.2.0
o Fixed bugs with SDP and short exons in spanned models
o Fixed bug with overwriting of some valid SDP span scores
o Fixed forward coordinates in GFF
o Added utr3,utr5 and cds fields to GFF output
o Fixed rounding bug in codonsubmat
(this prevented codon models working on some machines)
o Updated SDP codegen
o Fixed compilation to work with both glib-1 or glib-2
o Fixed phase macros
o Fixed build problems on OSF
o Added initial client/server code (nothing useful yet)
1.0.0 -> 1.1.0
o Replaced C4_Model_find_*() functions using names
o Fixed DP bug with non-local models
o Added Seeder and Match modules to support multi-hspset models
o Added %tcs etc to --ryo for dumping coding sequences
o Added CodonSubmat module
o Changed WordHood to work in codon space
o Changed Intron and Phase models to support joint introns for g2g
o Fixed bug with display of selenocysteine containing alignments
o Added --annotation option for cd2g model
o Fixed bug with introns in cigar strings
o Modified configure.in to compile cleanly on solaris
o Changed to use abstract sequences (requires optimisations)
o Fixed bug with --bestn tiebreaking
o Fixed bugs with suboptimal SDP alignments
o Simplified tracebacks for SDP
o Fixed bug with adjacent phased introns
o Added --codongapopen and --codongapextend
o Added new softmasking implementation
0.9.1 -> 1.0.0
o Added code for sdp over spanned models
o Added initial code for UTR model
o Fixed various minor bugs
o Improved error reporting
o Added --fastasuffix option for filtering directory contents
o Made installation of utilities optional
o Fixed memory bug with --percent option
o Improved build system
0.9.0 -> 0.9.1
o Fixed memory leak with SDP
o Bug fix to handle selenocysteines
o Fixed bug with words missing from word neighbourhood
o Fixed minor bugs and altered alignment display
0.8.3 -> 0.9.0
o Added seeded dynamic programming modules
(does not yet work with models containing spans)
o Fixed --bestn to allow tiebreaking of identically scoring hits
o Fixed bug with lost error messages with --bestn
o Fixed bug with alignment display and --forwardcoordinates
0.8.2 -> 0.8.3
o Fixed memory leak with BSDP
o Added BSAM module for whole chromosome alignment
o Added VFSM method of alignment seeding
o Rewrote word neighbourhood code for larger neighbourhoods
o Added --silent to fastafetch
o Added --alignmentwidth for alignent formatting
o Added --quality option for BSDP filtering
o Fixed tricky bug with suboptimal alignments in BSDP
o Fixed bug with reporting revcomp --bestn hits
o Marked non-consensus splice sites in alignment display
o Fixed bug with coordinates in alignment display
o Added frameshifts and split codons to gff output
0.8.1 -> 0.8.2
o Optimised BSDP for repeat-rich genomic comparisons
o Fixed bug with intron phase bounds
o Added experimental BSDP repeat pruning algorithm
o Allowed input to be directories of fasta files
o Added example to the exonerate usage message
o Fixed bug in code generation
o Tightened span bounds
o Fixed a bug with Waterman-Eggert
o Removed old node_is_used code
o Fixed memory leak in phase model
o Added PCR product dumping to ipcress
o Fixed bug with softmasking translated sequences
o Sorted multiple input files on file size for --bestn performance
0.8.0 -> 0.8.1
o Added module for codon usage calculations
o Fixed bug with phase model shadows
0.7.2 -> 0.8.0
o Added support for Waterman-Eggert style suboptimal alignments
o Fixed bugs with Hughey-style DP traceback
o Fixed bugs with phase model
o Added option for alignment refinement
o Stopped glib error messages from dumping core
o Added --{query,target}chunk{id,total} for splitting up jobs
o Added start of test suite
o Fixed a bug with the shadow designation algorithm
o Added %e[ti] for equivalenced symbol counting
o Turned off --forcegtag by default
o Added query-specific score thresholds
o Added RangeTree-based HSP pairing algorithm
o Made Shadows go state->transition to fix span model problems
o Fixed BSDP to work properly with suboptimal alignments
o Fixed shadow propagation algorithm for derived models.
o Simplified phase model for new shadows
0.7.1 -> 0.7.2
o Moved transition shields to calc
o Fixed a bug caused by shadow designation clashing
o Added shadow to intron model to apply min/max intron limits
o Fixed bugs with 3:3 HSP filtering
o Added general speedups to HSP code
o Bug fix for guessing database type of large files
o Added coding2genome model
o Simplified intron model (fewer states)
o Fixed bugs with shadow assignment ordering
o Fixed compilation when G_GNUC_EXTENSION not defined
o Added option for aggressive HSP filtering
o Removed old terminal_data/secondary_data system for C4_Calc
o Added Alphabet type to replace Sequence_Type and handle masking
o Improved softmasking implementation
o Removed all use of gmodule and renamed Plugin as Codegen,
o Changed bootstrapper for faster linking
o Separated Viterbi code from Optimal module
o Made bootstrapper use C4_COMPILED_MODEL_LIST
o Added Model_Type module
o Fixed sorting of results (on score) with --bestn
0.7.0 -> 0.7.1
o Modularised code for frameshifts and intron phases
o Added support for DNA:DNA alignments at protein level
o Added Coding2Coding and started Genome2Genome model
o Added support for per-transition output with --ryo
o Made changes for compilation on OS-X
o Separated parameters for dna and protein level alignments
o Added dejavu exact repeat finding library (for reprobate)
o Fixed query softmasking and various other bugs
o Added speedups to approximate matching for ipcress
o Updated man pages
o Added transition shields to fix phase model problems
o Separated DP layout code from Optimal module
0.6.7 -> 0.7.0
o Imported various fasta format file processing utilities
o Added --intronpenalty
o Added shadow transitions to C4
o Added protein2genomic model
o Refactored DP core by addition of Optimal_Data
and replacement of various hacks with proper 4D row data.
o Refactored codegen to use a single viterbi function per plugin.
o Modified Optimal_PatternMatrix system to reduce length
of generated code and decrease compile time.
o Fixed bootstrapper to use C4_CC and C4_CFLAGS
o Changed WordHood generation algorithm to utilise
separate input and output alphabets.
o Changed FSM implementation to allow more control when combining
words which are redundant or subsequences of each other.
o Imported ipcress and reimplemented most of it to handle
mismatches, mixed length and redundant primers etc.
o Changed ./configure --enable-gprof to work
with profiling version of libc6
o Changed argument handling code to parse lists from command line
o Added CompoundFile module
o Made exonerate work with multiple sequence query and target files
o Added more info to man page for exonerate
o Wrote man page for ipcress
o Added more sequence checking when using assertions.
o Fixed bug with display of equivalenced Ns
o Fixed attribute fields and off-by-one coordinate bugs in GFF.
o Added --bestn option for best-in-genome type searches etc.
o Changed --scanquery to --forcescan and made default selection
automatic based on sizes of input files.
o Fixed to parse non-standard __DATE__ format on OS-X.
o Simplified HPair code by addition of SAR module.
o Simplified HSPset code by using HSP horizon
o Simplified DNA2Protein model
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
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