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RELEASE_NOTES
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==========================================
THE RELEASE NOTE OF BS-SEEKER2
==========================================
v2.0.3 - May 19, 2013
1. Fix bug in utils.py
2. Add UPDATE file
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v2.0.4 - July 29, 2013
1. Update README.md (Definition of ATCGmap format)
2. Fix the "None" output when no parameter
3. Fix error report when using wrong path for short reads aligner
4. MIT License
------------------------------------------
V2.0.5 - Nov 31, 2013
1. Fix bug in "bs_single_end.py" for "numbers_premapped_lst[0] += len(Unique_FW_C2T)"
2. Make the default aligner to Bowtie
3. Update the README file
4. "-r N" in call-methylation will only control Wiggle file
5. Change the output of pair-end mapping to the standard format of SAM file (the QNAME and FLAG fields)
6. The artificially synthesized bases at the ends of RRBS fragments are removed when removing the adapters
7. Add the total number of bases of uniquely mapped reads to the STDOUT
8. Support "end-to-end" alignment mode in the Galaxy version
9. Support input file in both TEXT or Compressed (.gz) format
10. "-m" allow both INT and FLOAT as input. Ex: '-m 5' or '-m 0.05'
11. Add mode information in output
------------------------------------------
V2.0.6 - Jun 9, 2014
1. Add/Revise option "-M"/"-U" for output multiple-/un-mapped reads
2. Fix a bug in "bs_seeker2-call_methylation.py".
In the version V2.0.5, CGmap file will show A, T, C, G sites; in this version and following,
CGmap file will only show the C and G sites (with enough coverage).
3. Fix a bug in the output format "BS_Seeker_1"
In the v2.0.5, the "BS_Seeker_1" format has 3 more columns than previous format defined in "BS Seeker (1)".
In this version, the "BS_Seeker_1" format is revised to be consistent with the one in "BS Seeker (1)".
New definition of "BS_Seeker_1" format is add in "README.md".
------------------------------------------
V2.0.7 - Sep 4, 2014
1. [bs_seeker2-call_methylation.py] : add the parameter "--rm-CCGG", in order to avoid the biased caused by
artifact methylated C at the ends of fragments
2. [bs_seeker2-align.py] : Fix bugs under related with the parameter "--unmapped".
3. [bs_seeker2-call_methylation.py] : round the "methylation level" to 2-digits in all the output (ATCGmap, CGmap,
wiggle) formats
------------------------------------------
V2.0.8 - Sep 7, 2014
1. [bs_align/*.py] : Fix bug with "-m" and "-u" when splitting large input files internally.
2. [bs_seeker2-align.py] : Update the help information
------------------------------------------
V2.0.9 - Dec 30, 2014
1. [bs_seeker2-call_methylation] : Add the parameter "--rm-overlap", the overlapped region of two mates in
paired-end library will be counted only once.
2. [bs_seeker2-call_methylation] : All the first line "type wiggle_0" for wiggle output
3. [bs_seeker2-call_methylation] : Modified codes for speed improvements
4. [bs_seeker2-call_methylation] : Add the parameter"--sorted"
5. [bs_align/*.py] : Fix input empty line problem
------------------------------------------
V2.0.10 - Nov 5, 2015
1. [bs_seeker2-align.py] : Fix bug with "-s" and "-e"
2. [bs_seeker2-call_methylation.py] : Fix error with pysam version higher than 0.8.0
------------------------------------------
V2.1.0 - Dec 9, 2016
1. fixed bug related with pysam version
2. fixed bug related with output information
------------------------------------------
V2.1.1 - Apr. 13, 2017
1. [bs_seeker2-call_methylation.py] : fixed bug related with pysam version
2. [bs_seeker2-call_methylation.py] : modified output strategies
------------------------------------------
V2.1.2 - Jun. 23, 2017
1. [bs_seeker2-align.py] : Add option "--XSteve", alternative filtering method proposed by Prof. Steve Jacobson
------------------------------------------
V2.1.3 - Oct. 25, 2017
1. [bs_seeker2-call_methylation.py] : Add option "-d", allow user-defined highest coverage.
------------------------------------------
V2.1.4 - Nov. 13, 2017
1. [bs_align/bs_align_util.py] : fix bug in function of getting methylation levels for one read
------------------------------------------
V2.1.5 - Dec. 21, 2017
1. [bs_seeker2-build.py] : fix bug in finding genome file
------------------------------------------
V2.1.6 - Feb. 1, 2018
1. [bs_seeker2-build.py] : support built-in option for bowtie-build and bowtie2-align
------------------------------------------
V2.1.7 - Oct. 23, 2018
1. [bs_utils/utils.py] : fix a bug in chromosome name such as converting '.' to '_'
------------------------------------------
V2.1.8 - Oct. 30, 2018
1. [ThreadFasta & ChangeCoordicate] : provide solution for solving the large number of scaffold problem