Add seq_names and num_seqs functions to faidx.

Cargo.toml

@@ -36,7 +36,7 @@ url = "2.1"
 bindgen = ["hts-sys/bindgen"]
 bzip2 = ["hts-sys/bzip2"]
 curl = ["hts-sys/curl"]
-default = ["bzip2", "lzma", "curl"]
+default = ["bzip2", "lzma", "static"]
 gcs = ["hts-sys/gcs"]
 libdeflate = ["hts-sys/libdeflate"]
 lzma = ["hts-sys/lzma"]

src/bam/pileup.rs

@@ -81,6 +81,11 @@ impl<'a> Alignment<'a> {
         }
     }
 
+    /// Position within the read. Returns the value even if is_del or is_refskip
+    pub fn qpos_raw(&self) -> usize {
+        self.inner.qpos as usize
+    }
+
     /// Insertion, deletion (with length) if indel starts at next base or None otherwise.
     pub fn indel(&self) -> Indel {
         match self.inner.indel {

src/bcf/record.rs

@@ -981,19 +981,22 @@ impl Record {
         };
         let tag_c_str = ffi::CString::new(tag).unwrap();
         unsafe {
-            if htslib::bcf_update_info(
+            let code = htslib::bcf_update_info(
                 self.header().inner,
                 self.inner,
                 tag_c_str.as_ptr() as *mut c_char,
                 c_str.as_ptr() as *const ::std::os::raw::c_void,
                 len as i32,
                 ht as i32,
-            ) == 0
-            {
+            );
+            if code == 0 {
                 Ok(())
             } else {
                 Err(Error::BcfSetTag {
-                    tag: str::from_utf8(tag).unwrap().to_owned(),
+                    tag: format!(
+                        "Error {} with code {code}",
+                        str::from_utf8(tag).map_or_else(|_| format!("{tag:?}"), |x| x.to_owned())
+                    ),
                 })
             }
         }

src/faidx/mod.rs

@@ -83,6 +83,18 @@ impl Reader {
         Ok(cseq.to_bytes())
     }
 
+    pub fn num_seqs(&self) -> i32 {
+        unsafe { hts_sys::faidx_nseq(self.inner) }
+    }
+
+    pub fn seq_names(&self) -> Option<Vec<String>> {
+        let mut ret = Vec::new();
+        for seq in (0..self.num_seqs()).map(|x| self.seq_name(x)) {
+            ret.push(seq.ok()?);
+        }
+        Some(ret)
+    }
+
     /// Fetches the sequence and returns it as string.
     ///
     /// # Arguments