1.0.13: Jan 12, 2009
	- Included <cstring> so that g++ v4.3 can compile. Thank Yu Zhou and Matthias Zytnicki for pointing it out.
	- Added a simple Makefile

1.0.12: Nov 20, 2008
	- Fixed the bug that some matches may be missing at the end of a transcript. Thank Philipp Berninger for pointing it out.	

1.0.11: Nov 19, 2008
	- Fixed the bug that some matches may be missing with /output_alignment
	- Fixed the bug that outputs wrong trans_coord on reverse strand with /allow_insdel. Thank Robel Kahsay for pointing it out.

1.0.10: Nov 11, 2008
	- Fixed the bug that outputs 1bp off trans_coord on reverse strand with /allow_insdel. Thank Fuhong He for pointing it out.

1.0.9: Nov 2, 2008
	- Fixed /cut does not work for regions longer than 31bp bug. Thank Song Liu for pointing it out.

1.0.8: Aug 20, 2008
	- Added /zero_indexed
	- /eland:2 by default, added /output_all_matches
	- /both_strands by default, added /forward_strand
	- /remove_probes_with_many_targets deprecated
	- /mismatch_pos deprecated
	- /match_N by default, added /skip_N
	- reduced memory usage and improved speed
	- Detect repeated probes
	- Target count limit 255 deprecated, now unlimited
	- refined error/warning messages, and command line options
	- /match_longer_probes by default
	- Added /cut, removed /probe_len
	- Automatically detect probe_len
	- support stanford FASTA format, and raw DNA sequence file as input
	- Fixed bugs
	- Refined documents	

1.0.7: July 11, 2008
	- Fixed a bug of regular output and /match_longer_probes. Thank Xiangfeng Wang for pointing it out.
	- Fixed /eland:2 output bug
	- Improve speed and reduce memory usage
	- Not duplicate probes by default
	- /eland:2 by default

1.0.6: July 8, 2008
	- Fixed a bug of /eland. Thank Xiangfeng Wang for pointing it out.

1.0.5: July 8, 2008
	- Made /match_N, /match_longer_probes and /match_shorter_probes independent of /eland
	- performance Slightly improved for /eland

1.0.4: June 28, 2008
	- Fixed a bug of wrong trans coord in 1.0.3

1.0.3: June 27, 2008
	- Can handle long probes
	- Can handle short probes
	- Can handle N
	- Fix bug at the end of transcripts

1.0.2: June 19, 2008
	- Update help
	- Add Eland output format

1.0.1: February 12, 2008
	- Write HISTORY.txt file.

1.0.0: February 11, 2008
	- Put online.

0.1.7: July 28, 2007 to 0.1.76-October 15, 2007
	- Enable 5 insdels.
	- Remove probes with many targets, improve speed.
	- Add fast_index_fraction.
	- Add mask0_tables, improve speed.
	- Fix duplicate output bug.
	- Split longer probes.
	- Filter probes.
	- Truncate longer probes.
	- Output mismatched positions.
	- Output local alignment in results.
	- More accurate time estimation.
	- Add time and memory usage estimation.
	- Enable 3 insdels.
	- Add insdel support.
	- Determine 32 or 64 bit system and choose appropriate algorithms accordingly.
	- Output in probe order.
	- Put function to inline, improve speed.
	- Fix time measure on mac.
	- Fix available_memory_size on mac.
	- Search both strands.
	- Optimize mask_key, probe_search, mismatch, shifting, interpolation_search, etc.
	- Optimize number of probe lists.
	- Refine memory usage.	
	- Test with real data.
	- Do profiling, improve speed.
	- Input file error detect.
	- Deal with one N in the sequence.
	- Fix memory leak.
	- Fix bug when mismatch=5.

0.1.0: July 28, 2007
	- Put source tree into svn.

0.0.7: May 30, 2007
	- Put main functions to probe_match.h.

0.0.6: May 8, 2007
	- Implement shift_mask, store_key, sort_probes, interpolation_search, limit_num_part, etc.

0.0.5: May 7, 2007
	- Reduce memory usage.

0.0.4: March 21, 2007
	- Use index-filtering algorithm.

0.0.3: March 21, 2007
	- Use stl hash_map.

0.0.2: March 20, 2007
	- Enable 5 mismatches

0.0.1: February 27, 2007
	- Joaat hash and bloom filter based version, 2 mismatches maximum.