release: 1.11
2008-7-17
1.Fixed c stdlib error when compiler is gcc-4.3+.

release: 1.10
2008-04-21
1.Fixed a bug in dealign.cpp.
2.Updated the install function in makefile. 

release: 1.09
2008-04-09
1.Fixed a bug which will miss some 2 snp reads.
2.Fixed a bug which will miss some paired hits.

release: 1.08
2008-03-24
1. Fixed a bug in "dealign.cpp".

release: 1.07
2008-03-18
1. Added an option '-y' of pair-end alignment.

release: 1.06
2008-03-13
1. Fixed a bug which will rarely overflow on alignment of mRNA tags;


release: 1.05
2008-02-27
1. Fixed a bug which will report some false deletions;
2. Revised the program interface to be more clear to users;
3. More detailed description on Readme.

release: 1.04
2008-01-26
1. Fixed a bug on pair-end alignment which will miss some paired hits.
2. Fixed a bug which will report some wrong pairs.

release: 1.03
2008-01-03
1. Detected a small bug at reading reference.
2. Debugged soap.short, soap.contig, soap.huge throughly.

release: 1.02
2007-12-23
1. Reorganized makefile so that soap, soap.contig, soap.short and soap.huge will be generated on the same time;
2. Revised pair-end alignment. Paired hits and unpaired hits are putting on two independent output files now;
3. It will also iteratively trim low-quality 3'-end sequence for pair-end alignment to increase sensitivity.

release: 1.01
2007-11-23
1. Fixed a bug at removing equal hits;
2. Fixed a bug of repetitive calculation at some extreme cases;
3. Accelerate a little.

release: 1.0
Formal stable version.

release: 0.9.3
2007-10-23
1. Added -READ_60, since we are getting longer reads with high quality. So the maximum read length allowed is 60bp;
2. Implemented the function of iteratively trim low-quality ends during alignment;
3. Finally make the gapped alignment works. Small gaps (1~3bp) inside read is mappable;
4. Further revised the pairwise alignment modular. And we have tested it extensively in simulated data, but we will expect to have more revision after trying more on real data;
5. Some special function for miRNA and mRNA tag alignment was designed and implemented in this version;
6. Updated a little of the output format, provide more information in a user friendly way.

release: 0.9.2
2007-09-22
1. Added -READ_48, so now the maximum read length allowed is 48bp.

release: 0.9.1
2007-08-23
1. Fixed a bug at hit comparison when sorting;
2. Added pes_dealign to summarize result;

release: 0.9
2007-07-01
1. After broadly internal test on real data, this is the first stable version for outside download.
