simplify stitching

Author: flying-sheep

src/align/stitch.rs

@@ -1,7 +1,7 @@
 //! Seed clustering and stitching via dynamic programming
 use crate::align::score::AlignmentScorer;
 use crate::align::seed::Seed;
-use crate::align::transcript::Transcript;
+use crate::align::transcript::{CigarOpExt, Transcript};
 use crate::error::Error;
 use crate::index::GenomeIndex;
 use noodles::sam::alignment::record::cigar;
@@ -1754,6 +1754,16 @@ pub(crate) fn finalize_transcript(
 
     use cigar::op::{Kind, Op};
 
+    fn append_match(ops: &mut Vec<Op>, len: usize) {
+        if let Some(op) = ops.last_mut()
+            && op.kind() == Kind::Match
+        {
+            *op = op.with_added_len(len);
+        } else {
+            ops.push(Op::new(Kind::Match, len));
+        }
+    }
+
     // Build final CIGAR from exon blocks
     let mut final_cigar: Vec<Op> = Vec::new();
 
@@ -1779,14 +1789,7 @@ pub(crate) fn finalize_transcript(
                 // Shared match bases before the gap
                 let shared = read_gap.max(0) as usize;
                 if shared > 0 {
-                    // TODO: replace with “extend_or_push_match” function call
-                    if let Some(op) = final_cigar.last_mut()
-                        && op.kind() == Kind::Match
-                    {
-                        *op = Op::new(Kind::Match, op.len() + shared);
-                    } else {
-                        final_cigar.push(Op::new(Kind::Match, shared));
-                    }
+                    append_match(&mut final_cigar, shared);
                 }
                 let del = (genome_gap - read_gap.max(0)) as usize;
                 if del >= scorer.align_intron_min as usize
@@ -1800,14 +1803,7 @@ pub(crate) fn finalize_transcript(
                 // Insertion
                 let shared = genome_gap.max(0) as usize;
                 if shared > 0 {
-                    // TODO: replace with “extend_or_push_match” function call
-                    if let Some(op) = final_cigar.last_mut()
-                        && op.kind() == Kind::Match
-                    {
-                        *op = Op::new(Kind::Match, op.len() + shared);
-                    } else {
-                        final_cigar.push(Op::new(Kind::Match, shared));
-                    }
+                    append_match(&mut final_cigar, shared);
                 }
                 let ins = (read_gap - genome_gap.max(0)) as usize;
                 final_cigar.push(Op::new(Kind::Insertion, ins));
@@ -1818,27 +1814,13 @@ pub(crate) fn finalize_transcript(
         // This exon's match region
         let match_len = exon.read_end - exon.read_start;
         if match_len > 0 {
-            // TODO: replace with “extend_or_push_match” function call
-            if let Some(op) = final_cigar.last_mut()
-                && op.kind() == Kind::Match
-            {
-                *op = Op::new(Kind::Match, op.len() + match_len);
-            } else {
-                final_cigar.push(Op::new(Kind::Match, match_len));
-            }
+            append_match(&mut final_cigar, match_len);
         }
     }
 
     // Right extension match
     if right_extend.extend_len > 0 {
-        // TODO: replace with “extend_or_push_match” function call
-        if let Some(op) = final_cigar.last_mut()
-            && op.kind() == Kind::Match
-        {
-            *op = Op::new(Kind::Match, op.len() + right_extend.extend_len);
-        } else {
-            final_cigar.push(Op::new(Kind::Match, right_extend.extend_len));
-        }
+        append_match(&mut final_cigar, right_extend.extend_len);
     }
 
     // Right soft clip

src/align/transcript.rs

@@ -55,6 +55,15 @@ pub struct Exon {
     pub i_frag: u8,
 }
 
+pub(crate) trait CigarOpExt {
+    fn with_added_len(&self, len: usize) -> Self;
+}
+impl CigarOpExt for cigar::Op {
+    fn with_added_len(&self, len: usize) -> Self {
+        cigar::Op::new(self.kind(), self.len() + len)
+    }
+}
+
 fn cigar_char(kind: cigar::op::Kind) -> char {
     use cigar::op::Kind;
     match kind {

src/quant/transcriptome.rs

@@ -10,7 +10,7 @@
 //! only substantive divergence that rustar-aligner builds the transcript tables on
 //! the fly from the input GTF instead of loading persisted
 //! `transcriptInfo.tab`/`exonInfo.tab` files.
-use crate::align::transcript::{Exon, Transcript};
+use crate::align::transcript::{CigarOpExt, Exon, Transcript};
 use crate::error::Error;
 use crate::genome::Genome;
 use crate::junction::gtf::GtfRecord;
@@ -1301,8 +1301,7 @@ fn rebuild_cigar_without_softclips(
         if i == 0 && left_clip > 0 {
             // Fold left_clip into the first op if it's match-like.
             match op.kind() {
-                Kind::Match => out.push(Op::new(Kind::Match, op.len() + left_clip)),
-                Kind::SequenceMatch => out.push(Op::new(Kind::SequenceMatch, op.len() + left_clip)),
+                Kind::Match | Kind::SequenceMatch => out.push(op.with_added_len(left_clip)),
                 _ => {
                     // Extension landed on a non-match op (shouldn't normally
                     // happen).  Emit as Match.
@@ -1312,9 +1311,8 @@ fn rebuild_cigar_without_softclips(
             }
         } else if i + 1 == body.len() && right_clip > 0 {
             match op.kind() {
-                Kind::Match => out.push(Op::new(Kind::Match, op.len() + right_clip)),
-                Kind::SequenceMatch => {
-                    out.push(Op::new(Kind::SequenceMatch, op.len() + right_clip));
+                Kind::Match | Kind::SequenceMatch => {
+                    out.push(op.with_added_len(right_clip));
                 }
                 _ => {
                     out.push(*op);