skip over reads with invalid cigar

10XGenomics · Apr 21, 2021 · 3901805 · 3901805
1 parent de23b57
commit 3901805
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Showing 3 changed files with 9 additions and 5 deletions.
diff --git a/Cargo.lock b/Cargo.lock
diff --git a/Cargo.toml b/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "vartrix"
-version = "1.1.19"
+version = "1.1.20"
 authors = ["Ian Fiddes <[email protected]>", "Patrick Marks <[email protected]>"]
 edition = "2018"
 

diff --git a/src/main.rs b/src/main.rs
@@ -793,9 +793,13 @@ pub fn useful_alignment(haps: &VariantHaps, rec: &bam::Record) -> Result<bool, E
     let cigar = rec.cigar();
     for i in haps.locus.start..=haps.locus.end {
         // Don't include soft-clips but do include deletions
-        let t = cigar.read_pos(i as u32, false, true)?;
-        if t.is_some() {
-            return Ok(true);
+        match cigar.read_pos(i as u32, false, true) {
+            Ok(Some(_)) => return Ok(true),
+            Ok(None) => (),
+            Err(e) => {
+                info!("Skipping read {:?} due to invalid CIGAR: {}", rec, e);
+                return Ok(false);
+            }
         }
     }
     Ok(false)