Xclone

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- remove deprecated funcs
- update plotting tool, mainly in color settings
- update xclone tutorials in version 0.3.4
- BAF local phasing improvement
- BAF module support 3 and 5 allele bias states
- Combine module support prob correct mode for copy gain
- Combine module support prob correct mode for copy loss (default)
- update libratio capping and add cell filter limits
- use counts ratio as default
- libratio fitting update
- provide new denoise function (denoise by cluster)
- add ROC evaluation function in analysis module
- add functions for XClone clustering
- wrap independent plotting modules
- potential init to add predefined segmentation
- minor debug on BAF guide allele bias ratio
- add tutorials in xclone plotting
- add tutorials in xclone data analysis

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- Add tutorials for data loadding
- Wrap data loading for 3 main modules
- try supporting h5py higher version
- provide func to get results of different resolution (for benchmarking)
- updates in config: add default Smartseq_Config
- minor updates in other modules' configs and general configs
- BAF module update: feature specific concentration; extreme DP detection and rescaling(test)
- RDR module update: guide chr exclude chr X&Y
- more protecting steps in wrapped main module

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- fix bugs in loadding demo datasets

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- Wrap 3 main modules: RDR, BAF and Combine
- Add tutorials and documentations
- Provide demo data

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- Alpha version of XClone released