Changeset 3398

Timestamp:

Mar 25, 2015, 8:57:32 AM (8 years ago)

Author:

Peter

Message:

refs #794

Global arrays bam_nt16_stable and bam_nt16_rev_table in libbam have in
htslib changed name to seq_nt16_table and seq_nt16_str.

Introduce two functions that allow access to these arrays in a uniform
way regardless whether we are working against libbam or htslib.

Location:

trunk/yat/omic

Files:

• BamRead.cc (modified) (4 diffs)
• BamRead.h (modified) (1 diff)

trunk/yat/omic/BamRead.cc

@@ -228 +228 @@
   {
     int offset = 4*c.size() - 4*core().n_cigar;
-    
+
     reserve(data_size() + offset);
     /*
@@ -348 +348 @@
   char BamRead::sequence_str(size_t i) const
   {
-#if YAT_HAVE_HTSLIB
-    return seq_nt16_str[sequence(i)];
-#elif HAVE_BAM_NT16_REV_TABLE
-    return bam_nt16_rev_table[sequence(i)];
-#else
-    std::string table = "=ACMGRSVTWYHKDBN";
-    return table[sequence(i)];
-#endif
+    return nt16_str(sequence(i));
   }
 
@@ -374 +367 @@
     // copy sequence
     for (size_t i=0; i<seq.size(); ++i)
-#if YAT_HAVE_HTSLIB
-      sequence(i, seq_nt16_table[static_cast<size_t>(seq[i])]);
-#else
-      sequence(i, bam_nt16_table[static_cast<size_t>(seq[i])]);
-#endif
+      sequence(i, nt16_table(seq[i]));
     core().l_qseq = seq.size();
     // copy quality
@@ -442 +431 @@
   {
     std::swap(bam_, other.bam_);
+  }
+
+
+  const unsigned char nt16_table(char c)
+  {
+#if YAT_HAVE_HTSLIB
+    return seq_nt16_table[static_cast<uint8_t>(c)];
+#else
+    return bam_nt16_table[static_cast<uint8_t>(c)];
+#endif
+  }
+
+
+  const char nt16_str(uint8_t x)
+  {
+    assert(x<16);
+#if YAT_HAVE_HTSLIB
+    return seq_nt16_str[x];
+#elif HAVE_BAM_NT16_REV_TABLE
+    return bam_nt16_rev_table[x];
+#else
+    char table[16] = "=ACMGRSVTWYHKDBN";
+    return table[x];
+#endif
   }
 

trunk/yat/omic/BamRead.h

@@ -325 +325 @@
     const int& data_size(void) const;
   };
+
+  /**
+     Convert nucleotide character to 4-bit encoding.  The result is
+     encoded as 1/2/4/8 for A/C/G/T or combinations of these bits.
+
+     This is the same functionality that is provided in HTSLIB's
+     global array \c seq_nt16_table, but this function works also when
+     building against libbam. In libbam the array was called \c
+     bam_nt16_table.
+
+     This is the inverse of function nt16_str.
+
+     \since New in yat 0.13
+  */
+  const unsigned char nt16_table(char);
+
+  /**
+     Convert a 4-bit encoded nucleotide to a character.
+
+     This is the same functionality that is provided in HTSLIB's
+     global array seq_nt16_str, but this function works also when
+     building against libbam. In libbam the array was called \c
+     bam_nt16_rev_table.
+
+     This is the inverse of function nt16_table.
+
+     \since New in yat 0.13
+  */
+  const char nt16_str(uint8_t);
 
   /**