Changeset 3026

Timestamp:

Apr 6, 2013, 9:31:02 AM (9 years ago)

Author:

Peter

Message:

add function to modify a base quality (BamRead?). refs #746

Location:

trunk

Files:

• test/bam.cc (modified) (1 diff)
• yat/omic/BamRead.cc (modified) (1 diff)
• yat/omic/BamRead.h (modified) (2 diffs)

trunk/test/bam.cc

@@ -129 +129 @@
                 << " expected " << 8 << "\n";
   }
+  uint8_t q = bam.qual(24);
+  if (q != 72) {
+    suite.add(false);
+    suite.err() << "error: quality: " << static_cast<int>(q)
+                << " expected " << 72 << "\n";
+  }
+  uint8_t new_q = 60;
+  bam.qual(24, new_q);
+  q = bam.qual(24);
+  if (q != new_q) {
+    suite.add(false);
+    suite.err() << "error: quality: " << static_cast<int>(q)
+                << " expected " << new_q << "\n";
+  }
   test_cigar(suite, bam, in.header());
 }

trunk/yat/omic/BamRead.cc

@@ -166 +166 @@
 
 
+  void BamRead::qual(size_t i, uint8_t q)
+  { *(bam1_qual(bam_)+i)=q; }
+
+
   std::string BamRead::sequence(void) const
   {

trunk/yat/omic/BamRead.h

@@ -172 +172 @@
 
     /**
+       \brief set quality of a base
+
+       \param i base to modify
+       \param q new quality
+
+       \since New in yat 0.11
+     */
+    void qual(size_t i, uint8_t q);
+
+    /**
        \return query name
 
@@ -228 +238 @@
 
        \see bam_nt16_table
+
+       \since New in yat 0.11
      */
     void sequence(size_t i, uint8_t x);