adjusts indel CIGAR to better match bwa-meth

[bwlang]

This pull request fixes a bug in the left alignment of indels when using the --meth mode. Previously, indels were not always left-aligned according to SAM and VCF conventions due to the way methylation-aware base comparisons were handled. The update introduces a new function to correctly determine when bases can be considered equivalent during left alignment, improving compatibility and accuracy.

Bugfixes and Algorithm Improvements

• Added the mb_base_swap_ok function to correctly determine if swapping two bases across an indel preserves alignment score, accounting for methylation-aware equivalence (e.g., C<->T and G<->A) (align.c).
• Updated the indel left-alignment logic in mb_fix_cigar to use mb_base_swap_ok, ensuring indels are shifted left as far as possible under methylation-aware scoring (align.c).
• Modified the call to mb_fix_cigar in mb_update_extra to pass the scoring matrix, enabling methylation-aware base comparison during left alignment (align.c).

Documentation

• Added an entry in NEWS.md describing the bug, the fix, and the impact on alignment accuracy and compatibility with bwa-meth (NEWS.md).