Fix wavefront boundary with dynamic sequence length constraints

[unavailable-2374]

Summary

This PR fixes out-of-bounds access in the wavefront alignment algorithm by adding dynamic sequence length constraints during wave expansion.

Problem

Under certain conditions, the wavefront can expand beyond valid coordinate bounds, causing errors like:

Subrange 86,138 out of bounds (Get_Contig_Piece)

The static boundary constraints applied at the start of alignment functions are insufficient because the valid diagonal range changes as the anti-diagonal
progresses.

Solution

During each wavefront expansion step, calculate the effective diagonal range based on the current anti-diagonal position:

// Forward wave: anti-diagonal increases
int curr_anti = mida + 2*(dif+1);

// Reverse wave: anti-diagonal decreases
int curr_anti = mida - 2*(dif+1);

// Sequence length constraints
int seq_minp = curr_anti - 2*blen;  // ensures y <= blen
int seq_maxp = 2*alen - curr_anti;  // ensures x <= alen

// Take stricter constraint
int eff_minp = max(minp, seq_minp);
int eff_maxp = min(maxp, seq_maxp);

Changes

Applied dynamic bounds checking to all 6 wavefront functions:
- forward_wave, reverse_wave
- forward_wrap, reverse_wrap
- forward_extend, reverse_extend

Also restored simple boundary check: if (x < 0 || x < k)

Testing

Tested with the same assemblies that previously caused the 'Subrange out of bounds' error, and it now passes.