From 796705928240d0def07900b8b3d6235ea852e6df Mon Sep 17 00:00:00 2001
From: Nils Homer <nilshomer@gmail.com>
Date: Sun, 29 Mar 2026 22:56:16 -0700
Subject: [PATCH] fix: map unmapped reads (tid=-1) to correct index in
 slow_idxstats

When iterating CRAM records, unmapped reads have tid == -1. Casting
this to usize wraps to usize::MAX, causing an index-out-of-bounds
panic. Map tid == -1 to the designated unmapped slot at index nref.
---
 src/bam/mod.rs                    |  25 +++++++++++++++++++++----
 src/tbx/mod.rs                    |   4 ++--
 test/test_cram_unmapped.cram      | Bin 0 -> 1695 bytes
 test/test_cram_unmapped.cram.crai | Bin 0 -> 75 bytes
 4 files changed, 23 insertions(+), 6 deletions(-)
 create mode 100644 test/test_cram_unmapped.cram
 create mode 100644 test/test_cram_unmapped.cram.crai

diff --git a/src/bam/mod.rs b/src/bam/mod.rs
index 41fe6f134..d13852f90 100644
--- a/src/bam/mod.rs
+++ b/src/bam/mod.rs
@@ -846,8 +846,11 @@ impl IndexedReader {
                 return Err(Error::InvalidTid { tid });
             }
 
+            // Map unmapped reads (tid == -1) to the last slot (nref) to avoid usize wrapping.
+            let count_idx = if tid == -1 { nref } else { tid as usize };
+
             if tid != last_tid {
-                if (last_tid >= -1) && (counts[tid as usize][0] + counts[tid as usize][1]) > 0 {
+                if (last_tid >= -1) && (counts[count_idx][0] + counts[count_idx][1]) > 0 {
                     return Err(Error::BamUnsorted);
                 }
                 last_tid = tid;
@@ -858,7 +861,7 @@ impl IndexedReader {
             } else {
                 0
             };
-            counts[(*b).core.tid as usize][idx] += 1;
+            counts[count_idx][idx] += 1;
         }
 
         if ret == -1 {
@@ -1029,8 +1032,8 @@ impl Read for IndexedReader {
 impl Drop for IndexedReader {
     fn drop(&mut self) {
         unsafe {
-            if self.itr.is_some() {
-                htslib::hts_itr_destroy(self.itr.unwrap());
+            if let Some(itr) = self.itr {
+                htslib::hts_itr_destroy(itr);
             }
             htslib::hts_close(self.htsfile);
         }
@@ -3166,6 +3169,20 @@ CCCCCCCCCCCCCCCCCCC"[..],
         assert_eq!(expected, actual);
     }
 
+    #[test]
+    fn test_slow_idxstats_cram_unmapped() {
+        let mut reader = IndexedReader::from_path("test/test_cram_unmapped.cram").unwrap();
+        reader.set_reference("test/test_cram.fa").unwrap();
+        let expected = vec![
+            (0, 120, 2, 0),
+            (1, 120, 2, 0),
+            (2, 120, 2, 0),
+            (-1, 0, 0, 2),
+        ];
+        let actual = reader.index_stats().unwrap();
+        assert_eq!(expected, actual);
+    }
+
     // #[test]
     // fn test_number_mapped_and_unmapped_cram() {
     //     let mut reader = IndexedReader::from_path("test/test_cram.cram").unwrap();
diff --git a/src/tbx/mod.rs b/src/tbx/mod.rs
index 5994c49e3..18ea00bba 100644
--- a/src/tbx/mod.rs
+++ b/src/tbx/mod.rs
@@ -316,8 +316,8 @@ impl Read for Reader {
 impl Drop for Reader {
     fn drop(&mut self) {
         unsafe {
-            if self.itr.is_some() {
-                htslib::hts_itr_destroy(self.itr.unwrap());
+            if let Some(itr) = self.itr {
+                htslib::hts_itr_destroy(itr);
             }
             htslib::tbx_destroy(self.tbx);
             htslib::hts_close(self.hts_file);
diff --git a/test/test_cram_unmapped.cram b/test/test_cram_unmapped.cram
new file mode 100644
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GIT binary patch
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diff --git a/test/test_cram_unmapped.cram.crai b/test/test_cram_unmapped.cram.crai
new file mode 100644
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GIT binary patch
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literal 0
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