Previous versions of GMAP

• version 2007-07-16 (http://www.gene.com/share/gmap/src/gmap-2007-07-16.tar.gz)
  Major changes:
  • Bug fix for a rare fatal error
  • Fixed calculation of flanking regions
  • Augmented information in IIT files, including signed intervals, specific fields in annotations, and information to compute flanking intervals correctly. New IIT files have a different format. New GMAP programs will continue to work with the old IIT file format, but old GMAP programs will not work with new IIT formats.
• version 2007-06-04 (http://www.gene.com/share/gmap/src/gmap-2007-06-04.tar.gz)
  Major changes:
  • Allowing skipping of internal exons that don't match genome (e.g., in cross-species alignments)
  • Changed meaning of -X flag. Now indicates heavy favoring of canonical and semi-canonical introns
  • Added coverage and identity information to GFF3 output
  • Fixed GFF3 output so protein sequence is in-frame
  • Fixed PSL output so query and target gaps are consistent with block starts and lengths
  • Better parsing of NCBI genome headers in gmap_setup
  • Improvements in approximate alignment algorithm
  • Various bug fixes, including some fatal bugs and excessive memory usage in some cases
• version 2006-12-18 (http://www.gene.com/share/gmap/src/gmap-2006-12-18.tar.gz)
  Major changes:
  • Improvements in aligning low-identity sequences
  • Pruning of spurious exons at ends of alignment, and added -k flag to gmap to control this
  • Fixed minor bugs in translations by gmap
  • Now able to handle nucleotide U (representing T) in query sequence
  • Made strict translation of cDNA sequence the default. Added -Y flag to gmap to perform tolerant translation that corrects for frameshifts
  • Added -p flag to gmap to control pruning of poor or repetitive sequences
  • Change to output format of Coverage field, which now reports query length and trimmed query coordinates
  • Support for GFF files: GMAP can now output in GFF gene format (-f 2 flag) and match format (-f 3 flag), and the IIT utilities can now parse GFF files
  • New output type for gmap: IIT FASTA format (-f 8 flag)
  • GMAP mapping facility (-m flag) can now use IIT files with chromosomal coordinates and tags, in addition to those with universal coordinates and strand tags
  • Added printing of chromosomal subsets by get-genome
  • Added -u flag to get-genome and iit_get to print flanking intervals
  • Provided long options and documentation, including --help, for IIT utilities
  • Fixed bug in iit_get for 32-bit machines which truncated coordinates at 31 bits
  • Improved parsing of .md files in gmap_setup
• version 2006-04-21 (http://www.gene.com/share/gmap/src/gmap-2006-04-21.tar.gz)
  Major changes:
  • Improvements in speed, sensitivity, and alignment quality
  • Added intron lengths to exon summary output
  • Changes in output format for reporting mutations (now called "Amino acid changes").
  • Added printing of chromosomal subset
  • Provided greater user control in limiting intron lengths
  • Simplified setup process for creating new GMAP databases. Now gmap_setup creates a Makefile.
  • Fixed problems with PSL output coordinates
  • Changed output in compressed output from "dir:unknown" to "dir:indet".
  • Improved map-only mode (-1 flag)
• version 2005-10-25 (http://www.gene.com/share/gmap/src/gmap-2005-10-25.tar.gz)
  Major changes:
  • Created two types of batch mode: one for indices only, and one for indices and genome. The -B flag now takes an argument.
  • Added instructions and options for gmap_setup to create a full, uncompressed genome, containing non-standard or lower-case characters
  • Fixed psl (BLAT) output format to create new blocks at indels
  • Improved handling of non-standard and lower-case characters, with ambiguous matches now being marked in the alignment
  • Added large file support during compilation
  • Added an option in fa_coords to treat each sequence as a separate chromosome
  • Changed gmap_setup to generate a Makefile
  • Fixed bug in handling chromosomes greater than 2 gigabytes in length
  • The intron gap parameter (-i flag) can now be arbitrarily large, and shows the entire intron if necessary
  • Added option to look up map IIT information for each exon
  • Get-genome can now look up map IIT files
  • Restored printing of strain information, if available
  • Added sense/antisense information to compressed output
• version 2005-07-15 (http://www.gene.com/share/gmap/src/gmap-2005-07-15.tar.gz)
  Major changes:
  • Added psl (BLAT) output format
  • Added a range format for get-genome
  • Fixed bug in cross-species alignment
  • Fixed bug in iterative handling of short exons
• version 2005-06-23 (http://www.gene.com/share/gmap/src/gmap-2005-06-23.tar.gz)
  Major changes:
  • Improvements to cross-species alignments
  • Introduced option for alignment to be truncated at coding region
  • Turned off default identification of microexons at sequence ends
• version 2005-05-20 (http://www.gene.com/share/gmap/src/gmap-2005-05-20.tar.gz)
  Major changes:
  • Fixed bug when multiple threads read a file that was not memory mapped
  • Database setup now properly handles contigs marked as reverse complement
  • Speed improvements to nucleotide-level dynamic programming
• version 2005-05-06 (http://www.gene.com/share/gmap/src/gmap-2005-05-06.tar.gz)
  Major changes:
  • Added check for repetitive cDNA sequences
  • Using oligomer-based method for trimming sequence ends
  • Indexing intervals other than 6 can be specified during database setup
• version 2005-03-11 (http://www.gene.com/share/gmap/src/gmap-2005-03-11.tar.gz)
  Major changes:
  • Introduced concept of chromosomal subsets
  • By default, get-genome now prints just reference strain
  • List of contigs now indicates if reverse complement was needed
  • Mapping algorithm uses dangling matches to determine whether to sample further