[1.0.0] - 2017-03-29

Added

• Input parameter support with getopt in main.
• Auxillary intermediate data aux subfolder.
• Counts of reads filtered from SAM in the summary.
• Command line saved in aux/CMD file.
• X/Y chromosomes filter during SAM filter step.
• MAPQ level in SAM filter output.
• SAM filter step log.
• UMI preparation step log.
• Header line to bed file.
• Global centrality script.
• Cumulative of ratio and ratio of cumulative approaches to global centrality script.
• Properly formatted bed files per condition.

Changed

• File location, moved code to bin subfolder.
• Output structure, moved conditions into conditions subfolder.
• Output structure, moved output plots into plots subfolder.
• Read trimming script, optimized.
• Main script, now using modules.
• File structure, moved scripts to separate folder.
• Pos2cutsite script, optimized by calculating distance only from the 2 closest cutsite.
• Bed creation, moved to separate script.
• Barcode sequence option, moved to pat_files.

Fixed

• Read trimming.
• rmX/rmY option report.