Nanomonsv

- VCF format modifications.
- Bug fixes on VCF conversion errors.
- Optimizations for consensus generation and realignment validation steps.
- Modified bugs on breakpoint identifications.

- Add --simple_repeat_bed option in get function
- Organized package structure
- Support BAM files aligned with the -eqx option
- Abolish annot_utils in insert_classify function

- Add --simple_repeat_bed option in get function
- Organized package structure

- Support BAM files aligned with the -eqx option
- abolish annot_utils in insert_classify function

- Dealing with the issue of some SVs not being detected properly when the reference genome contains lowercase letters

- Implement the support for duplex reads.
- Improved breakpoint detection by modifying a one-time Smith-Waterman algorithm.
- Tune-up parameters for each preset (--qv10, qv15, qv20, qv25) for breakpoint detection in one-time smith-waterman algorithm.
- Improved the logic for breakpoint detection for overlapped alignment.