version 2013-08-19

http://research-pub.gene.com/gmap/src/gmap-gsnap-2013-08-19.tar.gz

Changes since 2013-08-15:
- In SAM output, putting HD header line before PG
- Fixed infinite loop in some GMAP-based alignments in GSNAP

Changes since 2013-08-14:
- Fixed SAM output in some GMAP cases involving complex alignments

Changes since 2013-07-20:
- In SAM output, printing PG and HD header lines
- Removing terminal alignments with excess mismatches
- Fixed rare fatal bug in GSNAP alignments that cross chromosomal boundaries
- Favoring local alignments over chimeric alignments in GMAP

Changes since 2013-07-16:
- Minor changes in preferences among alignments involving different insert lengths and splice probabilities
- Restored default terminal-threshold for DNA-Seq alignment, because terminal alignments are needed for some GMAP alignments

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
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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)))))