Main fixsnakemake

[Congm12]

• In case spaceranger outputs contain unzipped barcodes.tsv instead of barcodes.tsv.gz, add a check in calicos.smk to handle both cases.
• In case the cellsnp-lite and eagle2 outputs contain a large number of SNPs and spots/cells that can't be loaded in a dense matrix, the utils/get_snp_matrix.py code in the preprocessing step is updated to combine eagle2 phasing into cellsnp-lite genotyping using all sparse matrix operations, which eventually outputs eagle2-phased A allele count and B allele count sparse matrices.