version 2012-07-20 v3

http://research-pub.gene.com/gmap/src/gmap-gsnap-2012-07-20.v3.tar.gz

Changes in v3 compared with v2:
- 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

Change in v2 compared with v1:
- Fixed issue in GMAP where coordinates can go beyond chromosomal bounds for chimeric alignments

Major changes to GSNAP:
- Limiting suboptimal alignment search, to achieve greater speed
- Added flag --sam-multiple-primaries to allow multiple alignments to be marked as primary (useful for alignment to a transcriptome)
- Handling old Illumina FASTQ format for paired-end reads, ending in :0 or :1
- In cases of multiple, equally optimal alignments, ranking them by chromosome number and secondarily by chromosomal position
- Better checking for coordinates extending past chromosomal bounds
- Improved detection of translocations within read ends
- Not using trimmed-off part of terminal alignments to compute MAPQ scores
- Added flag --gmap-min-coverage to require GMAP hits to meet a minimum coverage threshold
- Fixed rare bug in missing nucleotides at ends of alignments
- Fixed bug in SAM output involving unpaired alignments with one end being a GMAP alignment, resulting in an incorrect mate chr
- Implemented Goby 2.0 output format

Major changes to GMAP:
- Limiting suboptimal alignment search, to achieve greater speed
- Changed from end-scanning strategy to a sampling strategy for initial mapping
- Performing oligomer chaining and dynamic programming by looking up genomic nucleotides as needed, rather than extracting the entire genomic segment
- Implemented iterative strategy to help find gene fusions
- In SAM output, using a Bayesian calculation of mapping quality scores, so multiple, equally good alignments get low scores
- Added --cmet-stranded and --cmet-nonstranded flags to allow alignment of bisulfite-treated sequences
- Better checking for coordinates extending past chromosomal bounds

Major changes to utilities:
- Improved speed of gmap_build when k-mer size is equal to base size
- Added -E flag to make gtf_splicesites, gtf_introns, and gtf_genes follow the exon_number field in GTF file, which was previously the default behavior. Now the default is for these utilities to determine their own exon ordering.
- Fixed psl_introns program so it produces output
- Changed GFF3 output to use lower-case coverage and identity tags
- Added long flag names to gmap_build
version 2013-03-12

http://research-pub.gene.com/gmap/src/gmap-gsnap-2013-03-12.tar.gz

Note: this version appears to be relatively stable, and addresses all bugs reported since version 2012-07-20.
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:
- 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:
- 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