version 2013-03-31 v5

http://research-pub.gene.com/gmap/src/gmap-gsnap-2013-03-31.v5.tar.gz

Changes since 2013-03-27:
- Fixed fatal bug in GMAP in solving short exons
- Fixed some bugs in GSNAP in aligning known splices at ends of alignments
- Fixed bug in GSNAP causing an unexpected pairtype
- Fixed bug in GMAP involving a memory error in some situations

Changes since 2013-03-21:
- Using terminal_threshold in filtering GMAP alignments with long soft clipping
- Added PG:Z:T field to indicate terminal alignment
- Allowing FASTA input file to be paired
- Considering alignments with long introns to be consistent if they are within the distance provided for that splice site in the known splicing file
- Fixed fatal bug in GMAP caused by division by 0
- Improved some alignments at ends of short reads in GSNAP

Changes since 2013-03-12:
- Added stringency in applying known splices
- Added better filters for GMAP alignments

Changes since 2013-03-05:
- Fixed alignments in GMAP involving dual breaks
- Fixed code in GMAP for finding shifted splice sites
- Fixed bug in GSNAP where --adapter-strip=off had no effect
- Added --force-single-end flag to GSNAP

Changes since 2013-02-25:
- Fixed memory bugs in GMAP when finding chimeric alignments
- Improved terminal finding algorithm in GSNAP
- gmap_build now allows filenames to contain spaces
- The --distant-splice-identity flag now works in GSNAP

Changes since 2013-02-15:
- Improved some paired-end alignments involving terminals on one end
- Fixed a bug in circular alignments that also involve trimming

Changes since 2013-02-05:
- Fixed a bug that could cause GSNAP to miss a translocation.
- Fixed a bug in finding terminal alignments, leading to bad alignments.

Change since 2013-01-23:
- Fixed compiler warnings from a static analysis of the code, but these situations should be rare or not occurring in practice.

Major changes to GSNAP and GMAP since 2012-07-20:
- Enabled alignment for circular chromosomes
- Favoring shorter introns at ends
- Trimming query N's at ends of alignments, so they do not imply a false extension
- Minor improvements in alignment accuracy
- In SNP-tolerant alignment, removed more biases that favor the reference genome over the alternate genome
- In SNP-tolerant alignment, fixed cases where genomic Ns were being treated as wildcard characters
- Added --novelend-splicedist to control allowed splice distance at ends for novel splicing
- Added --append option to append results to output files when --split-output is used
- Added --md-lowercase-snp to print allelic differences as lower case when they correspond to known variants
- Added --force-xs-dir flag to eliminate XS:A:? fields in SAM output
- Added XW and XV flags to SAM output when SNP-tolerant alignment is used
- For --pairalign mode in GMAP, multiple pairs of sequences can be provided
- Added --bunzip2 flag for uncompressing files compressed with bzip2
- Fixed bug where SAM headers were duplicated in .nomapping output file
- Added PG:Z:M flag to indicate which alignments were based on the GMAP method

Major changes to utilities since 2012-07-20:
- Fixed snpindex for sampling intervals other than 3.
- Fixed snpindex for cases where there is no gammaptrs file
- Fixed snp labels on warning messages produced by snpindex
- Implemented circular chromosomes in gmap_build
- Removing cases in defective GFF3 files that imply a negative intron length
version 2013-07-16

http://research-pub.gene.com/gmap/src/gmap-gsnap-2013-07-16.tar.gz

Changes since 2013-07-14:
- Allowing GMAP to align sequences with large overlaps (more than 100 bp) past the ends of a chromosome

Changes since 2013-06-27:
- Fixed printing of SAM output for alignments to circular chromosomes
- Fixed iit_store so it works on all inputs
- Fixed gff3_splicesites and gff3_introns programs to work on GFF3 files without gene lines
- Supports large genomes (more than 4 billion bp)

Changes since 2013-06-26:
- Using 8-bit SIMD instructions in dynamic programming on small matrices when SSE4.1 is available
- Using 8-bit SIMD instructions for oligoindex allocation procedure
- Fixed standard GSNAP output for second query sequence of paired-end reads; error introduced in 2013-06-14

Changes since 2013-06-18:
- Fixed fatal bug in GMAP and GSNAP from dynamic programming routine

Changes since 2013-06-14:
- Fixed fatal bug in GMAP and GSNAP from new SIMD instructions
- Added flag --allow-pe-name-mismatch to GSNAP

Changes since 2013-05-09:
- Changed default behavior in GSNAP of --terminal-threshold for DNA-Seq reads. Now terminal alignments are turned off by default.
- Added --expand-offsets option to independently control expansion of compressed offsets
- Using SIMD instructions to achieve significant increases in speed
- Faster handling of genomes with large numbers of contigs
- Occasional improvements in indel alignments
- Added checks for corrupted genomic index files
- Fixed computation of coverage for GFF output

Changes since 2013-04-30:
- Fixed SAM output for distant splicing (e.g., translocations)

Changes since 2013-03-31:
- Fixed rare fatal bug in GMAP in some chimeric alignments
- Fixed output of --clip-overlap feature in GSNAP for paired-end reads where the tails overlap
- Added flags --min-trimmed-coverage and --min-identity in GMAP for filtering of output
- Made GSNAP more sensitive for finding distant splices, especially in shorter reads of 50 bp or so
- Fixed fatal bugs in using --cross-species flag (also now called --find-shifted-canonical) in GMAP
- Fixed fatal bug in GSNAP when a known splice site was within a read length of the beginning of the genome