comparison BSseeker2/RELEASE_NOTES @ 1:8b26adf64adc draft default tip

V2.0.5

0:e6df770c0e58

v2.0.3 - May 19, 2013
1. Fix bug in utils.py
2. Add UPDATE file

1:8b26adf64adc

v2.0.3 - May 19, 2013
1. Fix bug in utils.py
2. Add UPDATE file

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