remove unuseed block aligner

cschin · Dec 18, 2023 · deef4cb · deef4cb
1 parent cd43d12
commit deef4cb
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Showing 3 changed files with 14 additions and 98 deletions.
diff --git a/build_no_agc_apple_slicon.sh b/build_no_agc_apple_slicon.sh
@@ -0,0 +1,14 @@
+#pushd WFA2-lib
+#make all
+#popd
+
+#rustup default stable
+rustup default stable-aarch64-apple-darwin
+cargo build -p pgr-db --release --no-default-features
+cargo build -p pgr-bin --release --no-default-features
+cargo install --path pgr-bin --no-default-features
+
+pushd pgr-tk/
+maturin build --release --no-default-features
+maturin build --release --skip-auditwheel --no-default-features
+popd
diff --git a/pgr-bin/Cargo.toml b/pgr-bin/Cargo.toml
@@ -21,7 +21,6 @@ bincode = { version = "2.0.0-rc.1", features = ["alloc"] }
 serde_json = "1.0.96"
 serde = "1.0.163"
 iset = "0.2.2"
-block-aligner = { version = "0.5", features = ["simd_avx2"] }
 
 [features]
 default = ["with_agc"]

diff --git a/pgr-bin/src/bin/pgr-generate-sv-analysis.rs b/pgr-bin/src/bin/pgr-generate-sv-analysis.rs
@@ -332,103 +332,6 @@ fn get_sw_aln_diff(s0str: &[u8], s1str: &[u8]) -> AlnDiff {
     wfa_aln_diff
 }
 
-use block_aligner::{cigar::*, scan_block::*, scores::*};
-fn get_block_aligner_diff(s0: &[u8], s1: &[u8]) -> AlnDiff {
-    let min_block_size = 256;
-    let max_block_size = 1024;
-
-    let nw: NucMatrix = NucMatrix::new_simple(1, -4);
-    let gaps = Gaps {
-        open: -3,
-        extend: -1,
-    };
-    let r = PaddedBytes::from_bytes::<NucMatrix>(s0, max_block_size);
-    let q = PaddedBytes::from_bytes::<NucMatrix>(s1, max_block_size);
-    let mut a = Block::<true, false>::new(q.len(), r.len(), max_block_size);
-    a.align(&q, &r, &nw, gaps, min_block_size..=max_block_size, 0);
-    let res = a.res();
-    // println!("score: {}", res.score);
-
-    let mut cigar = Cigar::new(res.query_idx, res.reference_idx);
-    a.trace()
-        .cigar_eq(&q, &r, res.query_idx, res.reference_idx, &mut cigar);
-    //println!("{}", cigar.to_string());
-    let mut p_t_match_end = 1_u32;
-    let mut p_q_match_end = 1_u32;
-    let mut t_pos = 0_u32;
-    let mut q_pos = 0_u32;
-    let mut cigar_vec = cigar.to_vec();
-    cigar_vec.push(OpLen {
-        op: Operation::Eq,
-        len: 0,
-    }); // Sentinel to trigger generating the last block
-    let diff = cigar_vec
-        .into_iter()
-        .flat_map(|oplen| match oplen.op {
-            Operation::Eq => {
-                let out = if t_pos >= p_t_match_end || q_pos >= p_q_match_end {
-                    if t_pos - p_t_match_end == q_pos - p_q_match_end && q_pos - p_q_match_end > 0 {
-                        let tvs =
-                            String::from_utf8_lossy(&s0[p_t_match_end as usize..t_pos as usize])
-                                .deref()
-                                .to_owned();
-                        let qvs =
-                            String::from_utf8_lossy(&s1[p_q_match_end as usize..q_pos as usize])
-                                .deref()
-                                .to_owned();
-                        Some((p_t_match_end, p_q_match_end, 'M', tvs.clone(), qvs.clone()))
-                    } else {
-                        let tvs = String::from_utf8_lossy(
-                            &s0[p_t_match_end as usize - 1..t_pos as usize],
-                        )
-                        .deref()
-                        .to_owned();
-                        let qvs = String::from_utf8_lossy(
-                            &s1[p_q_match_end as usize - 1..q_pos as usize],
-                        )
-                        .deref()
-                        .to_owned();
-                        if tvs.len() > qvs.len() {
-                            if !qvs.is_empty() {
-                                Some((p_t_match_end - 1, p_q_match_end - 1, 'D', tvs, qvs))
-                            } else {
-                                Some((p_t_match_end - 1, p_q_match_end - 1, 'E', tvs, qvs))
-                                // Error
-                            }
-                        } else if !tvs.is_empty() && tvs.len() < qvs.len() {
-                            Some((p_t_match_end - 1, p_q_match_end - 1, 'I', tvs, qvs))
-                        } else {
-                            Some((p_t_match_end - 1, p_q_match_end - 1, 'E', tvs, qvs))
-                            // Error
-                        }
-                    }
-                } else {
-                    None
-                };
-                t_pos += oplen.len as u32;
-                q_pos += oplen.len as u32;
-                p_t_match_end = t_pos;
-                p_q_match_end = q_pos;
-                out
-            }
-            Operation::I => {
-                q_pos += oplen.len as u32;
-                None
-            }
-            Operation::D => {
-                t_pos += oplen.len as u32;
-                None
-            }
-            Operation::X => {
-                t_pos += oplen.len as u32;
-                q_pos += oplen.len as u32;
-                None
-            }
-            _ => None,
-        })
-        .collect::<Vec<_>>();
-    AlnDiff::Aligned(diff)
-}
 
 fn aln_diff_to_records(
     rec: &CandidateRecord,