ChangeLog

2012-12-19 <chenhaosen@genomics.cn>
	* Release 1.1.1
	* (FilterProcessor.cpp) Change the method of determining low mean-quality for PE reads
		From:	Sum(Q)[read1,read2] / (len(read1)+len(read2)) < Threshold
		To:		Sum(Q)[read1]/(len(read1) < Threshold || Sum(Q)[read2]/(len(read2) < Threshold

2012-12-21 <chenhaosen@genomics.cn>
	* (PeBuffer.cpp::getReads) Initialize result1 and result2
	* (PeBuffer.cpp::readTask) Initialize result at very beginning 

2012-12-25 <chenhaosen@genomics.cn>
	* Release 1.1.2
	* Change deduplication module, replace BTree with std::map
	* (FilterProcessor) Use External sort and merge for low memory usage

2013-4-7 <jiangshuai@genomics.cn>
	* Release 1.2.0.2
	* sRNA module start outputing two files: small.txt, clean.txt
	* sRNA module, length distribution starts from 10
	* Change SRNACleanFA.cpp and SRNAProcessor.h

2013-4-9 <jiangshuai@genomics.cn>
	* Release 1.3.0
	* Tile-filter function added to FqBuffer and PeBuffer
	* Filter, FilterSRNA, FilterDGE modules support Tile-filter function 
	* Filter, FilterSRNA, FilterDGE modules all use FqBuffer and PeBuffer
	* When filtering tile, FilterSRNA and FilterDGE will not mandatory output anymore, while DNA remains the same

2013-4-9 <jiangshuai@genomics.cn>
	* Release 1.4.0
	* FilterMeta added

2014-9-10 <jiangshuai@genomics.cn>
	* Release 1.4.2
	* Upper limit of length changed to 512 for FilterMeta

2014-9-10 <jiangshuai@genomics.cn>
	* Release 1.4.2.1
	* Upper limit of length changed to 1024 for Filter

2014-10-14 <jiangshuai@genomics.cn>
	* Release 1.4.2
	* Bug fixed when determing seq length of read2
	* Bug fixed when outputing seq length of read2 in FilterProcessor.cpp

2015-01-05 <jiangshuai@genomics.cn>
	* Release 1.5 
	* Add --seqtype to process another name format
	* Add --polyatype for 2 methods of strip PolyA, 0 for AND, 1 for OR
	* Load adapterlist first and align adapter then
	* Filter index

2015-11-12 <lishengkang@genomics.cn>
	* Release 1.5.3
	* Add –cutAdaptor which cut adapters at ends of reads. Only reads shorter then –BaseNum will be aborted。 -cut will be ignored when applied this param
	* Add –BaseNum which used with -cutAdapter 
	* No more support of adapter list

2016-03-18 <lishengkang@genomics.cn>
	* Fix bug of keeping raw gz data open when filtering tile 

2016-04-25 <lishengkang@genomics.cn>
	* Release 1.5.4
	* Fix bug of low data volume when filtering SE data

2016-06-30 <lishengkang@genomics.cn>
	* Release 1.5.5
	* Add -3 to filter module, which accompanied with -d param to output duplicated reads while not counting them in QC stats

2016-08-22 <huangzhibo@genomics.cn>
	* Release 1.5.6
	* Add --fov which supporting filtering by FOV num in name of BGI-SEQ data, which can be used with --tile

2016-12-8 <huangzhibo@genomics.cn>
	* Release 1.6.0
	* Support compling for Windows
	* Support Streaming IO

2017-9-15 <chenyuxin@genomics.cn>
	* Release 1.6.2
	* Change CMakeList for automatic compling
	* Add Python script in assist of Streaming processing
	* Add plotting R-scripts for QC stats

2018-4-11 <chenyuxin@genomics.cn>
	* Release 1.6.3
	* Bug fixed of incompatibility between outType and Rmdup
	* Bug fixed when performing adapter cutting and length filtering
	* Add PolyX filtering function

2018-4-23 <chenyuxin@genomics.cn>
	* Release 1.6.4
	* Fullfil CMakeList
	* Add QC stats of trimming position
	* Optimize trimming algorithm
	* Fix most warning of compiling

2018-6-30 <chenyuxin@genomics.cn>
	* Release 1.6.5
	* Add low-Q filtering function to sRNA module
	* Bug fixed when filtering adapter
	* Add function of filtering contaminants

2018-8-17 <gongchun@genomics.cn>
	* Release 2.0 beta
	* Delete filterDGE module
	* Unify running logic of all modules, which mainly differ in adapter determination now.
	* Main pipeline includes counting raw data, filtering data and counting filtered data.
	* Merge params of modules. Default values mainly derive from filter module, so users should be cautious when using other modules.
	* filter and filterMeta modules support SE and PE, filtersRNA support SE only.
	* filter and filterMeta modules update adapter determination algorithms.
	* Have 2 running modes now: ssd and non-ssd. It is recommended to use ssd mode on high-speed IO storage(like SSD). Default to be non-ssd.
	* Remove deduplication function.
	* As thread number increases, running efficiency improves obviously. It costs 70 mins to process 1.3G reads (PE50) with 16 threads at non-ssd mode.

2018-12-1 <gongchun@genomics.cn>
	* Release 2.0.1
	* Bugs fixed
	* Change of split module for fastq files after filtering
	* Loose standard of determining adapters

2018-12-26 <gongchun@genomics.cn>
	* Release 2.0.2
	* Promise order consistent for multi-threading
	* Lower MEM and accelerate much

2019-1-10 <gongchun@genomics.cn>
	* Release 2.0.3
	* Bugs fixed of SE trimming 和 fov filtering

2019-2-1 <gongchun@genomics.cn>
	* Release 2.0.5
	* Add extraction function on filtered data.
	* Fix bugs of data loading

2019-3-31 <gongchun@genomics.cn>
	* Release 2.0.6
	* Fix the bug of unstead output
	* Optimize algorithms of global determination of contaminants

2019-5-17 <gongchun@genomics.cn>
	* Release 2.0.7
	* Fix bugs of running on MacOS and others

2019-6-28 <gongchun@genomics.cn>
	* Release 2.0.8
	* Update README to adapt to 2.X
	* Optimize the algorithm of filtering FOV

2019-7-24 <gongchun@genomics.cn>
	* Release 2.1.0
	* Change the output order to the same as input, which accelerate the split function
	* Add randomness of random extraction

2019-12-3 <gongchun@genomics.cn>
	* Release 2.1.1
	* Bugs fixed of SE trim、polyX and random extraction

2020-4-19 <gongchun@genomics.cn>
	* Release 2.1.2
	* Add filterHts module

2020-7-23 <gongchun@genomics.cn>
	* Release 2.1.3
	* Support adapter list as input
	* Add filterStLFR module
	* Fix bugs of adapter detection in filterHts module

2020-8-27 <gongchun@genomics.cn>
	* Release 2.1.4.beta.1
	* Bugs fixed

2020-11-27 <gongchun@genomics.cn>
	* Release 2.1.4.beta.3
	* add rmdup function by adopting reverse Bloom filter

2020-12-17 <gongchun@genomics.cn>
	* Release 2.1.5
	* add rmdup function by adopting reverse Bloom filter

2021-4-30 <gongchun@genomics.cn>
	* Release 2.1.6
    * Fix the bug of detecting adapter in the head of read
    * Increase the max threading num from 48 to 72

2022-1-16 <gongchun@genomics.cn>
	* Release 2.1.7
	* Fix the bug when totalReadsNum parameter is too large to do the extraction

2023-8-31 <gongchun@genomics.cn>
	* Release 2.1.8
	* Assign max value of Quality Score by parameter
	* Automatically set the max threading number by software
	* Max supported read length increased from 500 to 1000

2024-3-28 <gongchun@genomics.cn>
	* Release 2.1.9
	* Fix the bug of quality value getting out of bounds and some statistical values overflowing
	* Remove the obsolete description about parameter L
	* Add some description about usage of config file