Nanomonsv

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

- 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.

- Improved the logic of the validation step in response to feedback from 35.
- Introduced CRAM format support, as per feedback received in 38.
- Added parameter preset options (--qv10, qv15, qv20, qv25) for PacBio HiFi and ONT Q20+ chemistry.
- Enhanced the robustness of the single breakend SV module procedures, addressing bug 39.

- Improved the logic of the validation step in response to feedback from 35.
- Introduced CRAM format support, as per feedback received in 38.
- Added parameter preset options (--qv10, qv15, qv20, qv25) for PacBio HiFi and ONT Q20+ chemistry.
- Enhanced the robustness of the single breakend SV module procedures, addressing bug 39.

- Significantly (2~3 times or more) reduced computational costs by improving the logic that pre-filters unlikely somatic SV candidates during the clustering step.

- Fixed error due to using numpy old type (thanks to MartinezRuiz-Carlos 37).