Clippy fixes

Author: brainstorm

src/bam/record.rs

@@ -408,8 +408,7 @@ impl Record {
         // seq
         {
             for j in (0..seq.len()).step_by(2) {
-                data[i + j / 2] = ENCODE_BASE[seq[j] as usize] << 4
-                    | (if j + 1 < seq.len() {
+                data[i + j / 2] = (ENCODE_BASE[seq[j] as usize] << 4) | (if j + 1 < seq.len() {
                         ENCODE_BASE[seq[j + 1] as usize]
                     } else {
                         0
@@ -1689,14 +1688,14 @@ impl Cigar {
     fn encode(self) -> u32 {
         match self {
             Cigar::Match(len) => len << 4, // | 0,
-            Cigar::Ins(len) => len << 4 | 1,
-            Cigar::Del(len) => len << 4 | 2,
-            Cigar::RefSkip(len) => len << 4 | 3,
-            Cigar::SoftClip(len) => len << 4 | 4,
-            Cigar::HardClip(len) => len << 4 | 5,
-            Cigar::Pad(len) => len << 4 | 6,
-            Cigar::Equal(len) => len << 4 | 7,
-            Cigar::Diff(len) => len << 4 | 8,
+            Cigar::Ins(len) => (len << 4) | 1,
+            Cigar::Del(len) => (len << 4) | 2,
+            Cigar::RefSkip(len) => (len << 4) | 3,
+            Cigar::SoftClip(len) => (len << 4) | 4,
+            Cigar::HardClip(len) => (len << 4) | 5,
+            Cigar::Pad(len) => (len << 4) | 6,
+            Cigar::Equal(len) => (len << 4) | 7,
+            Cigar::Diff(len) => (len << 4) | 8,
         }
     }
 

src/bcf/header.rs

@@ -375,7 +375,7 @@ impl HeaderView {
             let n = (*self.inner).n[htslib::BCF_DT_ID as usize] as usize;
             let entry = slice::from_raw_parts((*self.inner).id[htslib::BCF_DT_ID as usize], n);
             let d = (*entry[id as usize].val).info[hdr_type as usize];
-            (d >> 4 & 0xf, d >> 8 & 0xf, d >> 12)
+            ((d >> 4) & 0xf, (d >> 8) & 0xf, d >> 12)
         };
         let _type = match _type as ::libc::c_uint {
             htslib::BCF_HT_FLAG => TagType::Flag,

src/bcf/record.rs

@@ -1202,7 +1202,7 @@ impl From<GenotypeAllele> for i32 {
             GenotypeAllele::Unphased(a) => (a, 0),
             GenotypeAllele::Phased(a) => (a, 1),
         };
-        (allele + 1) << 1 | phased
+        ((allele + 1) << 1) | phased
     }
 }