ensure seq.len() == qual.len() when set()ing bam::Record

CHANGELOG.md

@@ -5,6 +5,8 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 ## [0.26.1] - 2019-12-03
 ## Changes
 - Various bug fixes in CIGAR string handling, INFO tag reading and FORMAT tag reading.
+- bam::Record.set() will panic if seq.len() != qual.len(). Previously, mismatched length would cause
+  uninitialized memory to be written into the BAM file.
 
 ## [0.26.0] - 2019-09-27
 ## Changes

src/bam/record.rs

@@ -279,10 +279,17 @@ impl Record {
     /// Set variable length data (qname, cigar, seq, qual).
     /// Note: Pre-existing aux data will be invalidated
     /// if called on an existing record. For this
-    /// reason, never call push_aux() before set().
+    /// reason, never call push_aux() before set(). `qual` is Phred-scaled
+    /// quality values, without any offset.
+    /// NOTE: seq.len() must equal qual.len() or this method
+    /// will panic. If you don't have quality values use
+    /// `let quals = vec![ 255 as u8; seq.len()];` as a placeholder that will
+    /// be recognized as missing QVs by `samtools`.
     pub fn set(&mut self, qname: &[u8], cigar: Option<&CigarString>, seq: &[u8], qual: &[u8]) {
         self.cigar = None;
 
+        assert!(seq.len() == qual.len(), "seq.len() must equal qual.len()");
+
         let cigar_width = if let Some(cigar_string) = cigar {
             cigar_string.len()
         } else {