fix: various clippy issues

Author: jeeeesper

src/bam/record.rs

@@ -358,9 +358,9 @@ impl Record {
 
         let orig_aux_offset = self.qname_capacity()
             + 4 * self.cigar_len()
-            + (self.seq_len() + 1) / 2
+            + self.seq_len().div_ceil(2)
             + self.seq_len();
-        let new_aux_offset = q_len + extranul + cigar_width + (seq.len() + 1) / 2 + qual.len();
+        let new_aux_offset = q_len + extranul + cigar_width + seq.len().div_ceil(2) + qual.len();
         assert!(orig_aux_offset <= self.inner.l_data as usize);
         let aux_len = self.inner.l_data as usize - orig_aux_offset;
         self.inner_mut().l_data = (new_aux_offset + aux_len) as i32;
@@ -416,7 +416,7 @@ impl Record {
                     });
             }
             self.inner_mut().core.l_qseq = seq.len() as i32;
-            i += (seq.len() + 1) / 2;
+            i += seq.len().div_ceil(2);
         }
 
         // qual
@@ -564,7 +564,7 @@ impl Record {
 
     fn seq_data(&self) -> &[u8] {
         let offset = self.qname_capacity() + self.cigar_len() * 4;
-        &self.data()[offset..][..(self.seq_len() + 1) / 2]
+        &self.data()[offset..][..self.seq_len().div_ceil(2)]
     }
 
     /// Get read sequence. Complexity: O(1).
@@ -579,7 +579,7 @@ impl Record {
     /// This does not entail any offsets, hence the qualities can be used directly without
     /// e.g. subtracting 33. Complexity: O(1).
     pub fn qual(&self) -> &[u8] {
-        &self.data()[self.qname_capacity() + self.cigar_len() * 4 + (self.seq_len() + 1) / 2..]
+        &self.data()[self.qname_capacity() + self.cigar_len() * 4 + self.seq_len().div_ceil(2)..]
             [..self.seq_len()]
     }
 
@@ -787,7 +787,7 @@ impl Record {
                 // CIGAR (uint32_t):
                 + self.cigar_len() * std::mem::size_of::<u32>()
                 // Read sequence (4-bit encoded):
-                + (self.seq_len() + 1) / 2
+                + self.seq_len().div_ceil(2)
                 // Base qualities (char):
                 + self.seq_len()..],
         }

src/bcf/mod.rs

@@ -318,7 +318,7 @@ impl IndexedReader {
     /// # Arguments
     ///
     /// * `rid` - numeric ID of the reference to jump to; use `HeaderView::name2rid` for resolving
-    ///           contig name to ID.
+    ///   contig name to ID.
     /// * `start` - `0`-based **inclusive** start coordinate of region on reference.
     /// * `end` - Optional `0`-based **inclusive** end coordinate of region on reference. If `None`
     ///   is given, records are fetched from `start` until the end of the contig.
@@ -605,7 +605,7 @@ pub mod synced {
         /// # Arguments
         ///
         /// * `rid` - numeric ID of the reference to jump to; use `HeaderView::name2rid` for resolving
-        ///           contig name to ID.
+        ///   contig name to ID.
         /// * `start` - `0`-based start coordinate of region on reference.
         /// * `end` - `0`-based end coordinate of region on reference.
         pub fn fetch(&mut self, rid: u32, start: u64, end: u64) -> Result<()> {
@@ -835,6 +835,8 @@ fn bcf_open(target: &[u8], mode: &[u8]) -> Result<*mut htslib::htsFile> {
 
 #[cfg(test)]
 mod tests {
+    use tempfile::NamedTempFile;
+
     use super::record::Buffer;
     use super::*;
     use crate::bcf::header::Id;

src/bcf/record.rs

@@ -659,7 +659,7 @@ impl Record {
     /// # Arguments
     ///
     /// - `genotypes` - a flattened, two-dimensional array of GenotypeAllele,
-    ///                 the first dimension contains one array for each sample.
+    ///   the first dimension contains one array for each sample.
     ///
     /// # Errors
     ///
@@ -841,7 +841,7 @@ impl Record {
     ///
     /// - `tag` - The tag's string.
     /// - `data` - a flattened, two-dimensional array, the first dimension contains one array
-    ///            for each sample.
+    ///   for each sample.
     ///
     /// # Errors
     ///
@@ -856,7 +856,7 @@ impl Record {
     ///
     /// - `tag` - The tag's string.
     /// - `data` - a flattened, two-dimensional array, the first dimension contains one array
-    ///            for each sample.
+    ///   for each sample.
     ///
     /// # Errors
     ///
@@ -893,7 +893,7 @@ impl Record {
     ///
     /// - `tag` - The tag's string.
     /// - `data` - a flattened, two-dimensional array, the first dimension contains one array
-    ///            for each sample.
+    ///   for each sample.
     ///
     /// # Errors
     ///
@@ -934,7 +934,7 @@ impl Record {
     ///
     /// - `tag` - The tag's string.
     /// - `data` - a two-dimensional array, the first dimension contains one array
-    ///            for each sample. Must be non-empty.
+    ///   for each sample. Must be non-empty.
     ///
     /// # Errors
     ///

src/bgzf/mod.rs

@@ -121,10 +121,7 @@ impl std::io::Read for Reader {
             htslib::bgzf_read(self.inner, buf.as_mut_ptr() as *mut libc::c_void, buf.len())
         };
         if nbytes < 0 {
-            Err(std::io::Error::new(
-                std::io::ErrorKind::Other,
-                "Can not read",
-            ))
+            Err(std::io::Error::other("Can not read"))
         } else {
             Ok(nbytes as usize)
         }
@@ -268,10 +265,7 @@ impl std::io::Write for Writer {
         let nbytes =
             unsafe { htslib::bgzf_write(self.inner, buf.as_ptr() as *mut libc::c_void, buf.len()) };
         if nbytes < 0 {
-            Err(std::io::Error::new(
-                std::io::ErrorKind::Other,
-                "Can not write",
-            ))
+            Err(std::io::Error::other("Can not write"))
         } else {
             Ok(nbytes as usize)
         }
@@ -282,10 +276,7 @@ impl std::io::Write for Writer {
         if exit_code == 0 {
             Ok(())
         } else {
-            Err(std::io::Error::new(
-                std::io::ErrorKind::Other,
-                "Can not flush",
-            ))
+            Err(std::io::Error::other("Can not flush"))
         }
     }
 }