File: ChangeLog

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exonerate 2.4.0-5
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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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