message: WIP: use simple stripes in seed_alignment
diff: use crate::align::align::AlignPairwiseParams;
  +use crate::align::band_2d::simple_stripes;
  use crate::align::band_2d::Stripe;
  use crate::align::seed_match::seed_match;
  use crate::io::nuc::Nuc;
  @@ -6,6 +7,8 @@ use crate::make_error;
  use eyre::Report;
  use num_traits::{abs, clamp, clamp_min};
  +use super::band_2d::Band2d;
  +
  fn is_bad_letter(letter: Nuc) -> bool {
  letter == Nuc::N
  }
  @@ -99,10 +102,13 @@ pub fn seed_alignment(
  let band_width = (((ref_size + query_size) as f32 * 0.5) - 3.0).round() as usize;
  if band_width < (2 * params.seed_length) {
  + let mean_shift = ((ref_size as f32 - query_size as f32) * 0.5).round() as i32;
  + let stripes = simple_stripes(mean_shift, band_width, ref_size, query_size);
  +
  return Ok(SeedAlignmentResult {
  - mean_shift: ((ref_size as f32 - query_size as f32) * 0.5).round() as i32,
  + mean_shift,
  band_width,
  - stripes: vec![], // HACK: stripes are empty
  + stripes,
  });
  };
  @@ -128,17 +134,22 @@ pub fn seed_alignment(
  },
  );
  - let terminal_bandwidth: i32 = 20;
  - let excess_bandwidth: i32 = 9;
  - let stripes = make_stripes(qry_seq, ref_seq, params, terminal_bandwidth, excess_bandwidth);
  - println!("stripes, len {}", stripes.len());
  - println!("pos 0 {:?}", stripes[0]);
  - println!("pos 15000 {:?}", stripes[15000]);
  - println!("pos 29902 {:?}", stripes[29902]);
  + // let terminal_bandwidth: i32 = 20;
  + // let excess_bandwidth: i32 = 9;
  + // let stripes = make_stripes(qry_seq, ref_seq, params, terminal_bandwidth, excess_bandwidth);
  + // println!("stripes, len {}", stripes.len());
  + // println!("pos 0 {:?}", stripes[0]);
  + // println!("pos 15000 {:?}", stripes[15000]);
  + // println!("pos 29902 {:?}", stripes[29902]);
  +
  + let mean_shift = (0.5 * (min_shift + max_shift) as f64).round() as i32;
  + let band_width = (max_shift - min_shift + 9) as usize;
  +
  + let stripes = simple_stripes(mean_shift, band_width, ref_size, query_size);
  Ok(SeedAlignmentResult {
  - mean_shift: (0.5 * (min_shift + max_shift) as f64).round() as i32,
  - band_width: (max_shift - min_shift + 9) as usize,
  + mean_shift,
  + band_width,
  stripes,
  })
  }
  