Bug fix -- sailor bedfile position off by one error

Ensuring that Sailor bed files line up well with appropriate base when viewed in IGV. They were previously +1 higher than appropriate.

v1.0.1

What's Changed

• fix edgecase where gene names are reported as nan value by @byee4 in #62

Full Changelog: v1.0.0...v1.0.1

Release v1

• This release includes the ability to tabulate edits and reads across cells in adata format (saved as h5ad files)
• Increased test robustness and coverage enable more confidence in MARINE results
• MARINE can be run on bulk data, or single-cell data, with similar outputs explained in an updated, more detailed README

fix 15.a

Bug in coverage sparse matrix combination was fixed here.

sparse matrices generated for edits and coverage

• Added generation sparse edit matrices, for every edit type, such that edits can be read like:

edits_adata = sc.read_h5ad(f'{output_folder}/final_matrix_outputs/comprehensive_A_G_edits_matrix.h5ad')

and coverage can be read like:

reads_adata = sc.read_h5ad(f'{output_folder}/final_matrix_outputs/comprehensive_coverage_matrix.h5ad')

Updated parameters and ability to tabulate specified edits

• ability to tabulate coverage at specified edit sites across all cells in single cell mode

Speeding up single cell and enabling all cells

Leveraging awk to split the bed for samtools depth calculations.

Speed up for single cell coverage calculations

Using samtools depth now

Major improvement in bulk single-end speed

• samtools depth leveraged to calculate depths for all edited sites, rather than trying to multiprocess using pysam coverage methods

Bedgraph improvements

Ability to make sailor outputs and bedgraphs with multiple edit types.