wfa_sys.nim

import futhark
import std/typetraits

type CFile* = typeof(File.pointerBase)

importc:
  sysPath "/usr/lib/clang/13/include"
  path "./WFA2-lib"
  "wavefront/wavefront_align.h"
  rename FILE, CFile


converter toCint(x: int): cint =
   x.cint

var attr = wavefront_aligner_attr_default
attr.distance_metric = gap_affine
attr.affine_penalties.match = 0
attr.affine_penalties.mismatch = 2
attr.affine_penalties.gap_opening = 2
attr.affine_penalties.gap_extension = 1
attr.alignment_scope = compute_alignment

attr.memory_mode = wavefront_memory_high

attr.heuristic.strategy = wf_heuristic_wfadaptive;
attr.heuristic.min_wavefront_length = 10;
attr.heuristic.max_distance_threshold = 50;
attr.heuristic.steps_between_cutoffs = 1;

attr.alignment_form.span = alignment_endsfree;

attr.alignment_form.pattern_begin_free = 7
attr.alignment_form.pattern_end_free = 0
attr.alignment_form.text_begin_free = 11
attr.alignment_form.text_end_free = 0

attr.system.max_alignment_score = 1_000_000
attr.system.check_alignment_correct = false
attr.system.probe_interval_global = 3000
attr.system.probe_interval_compact = 6000
attr.system.max_memory_compact = uint64.high
attr.system.max_num_threads = 1
attr.system.max_memory_resident = uint64.high # Automatically set based on memory-mode
attr.system.max_memory_abort = uint64.high # Unlimited
attr.system.verbose = 0

   

let wf = wavefront_aligner_new(attr.addr)


#             0123456789012345678901234567890
var p =      "AAAAAAACCGGTTGGAAAAAAAAAAAAAAAAAA".cstring;
    #    0123456788901234
var t = "AAAAAAAAAAAACCGGTTGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA".cstring;

discard wavefront_align(wf, p, p.len, t, t.len)

echo "OK"

cigar_print_pretty(stderr, p, p.len, t, t.len,
    wf.cigar.addr, wf.mm_allocator)

wavefront_aligner_delete(wf)