Scsplit

changed PA matrix to RR/AA matrix
bug fixing - distinguishing variants detection in cases where not enough can be found for the whole matrix

Important bug fixing: fixed PCA n_component in previous release caused runtime error.

A few functional updates are included in this release:

main.py: former sc_split_main.py, new functions added to detect distinguishing alleles after samples are split, so that people can use them as a reference to get samples identified; command line arguments allowed
matrices.py: former sc_split_matrices.py, command line arguments allowed
genotype.py: former sc_split_vcf.py, command line arguments allowed
simulation.py: former sc_split_simu.py, command line arguments allowed
validate.py: newly added, users can use this to validate the genotypes based on the scSplit result compared to known vcf

This is the first release of scSplit as a genotype-free tool for demultiplexing pooled single cell samples.

This version of scSplit toolset contains below script:

sc_split_matrices.py: build SNV x barcode Matrices (reference and alternative alleles)
sc_split_main.py: main script to conduct reference free AF-based demultiplexing
sc_split_vcf.py: generate vcf file containing simulated genotypes according to demultiplexing assignments
sc_split_simu.py: simulate BAM and allele fraction matrices based on provided vcf and BAM reads