text: user1770: The SAM file format specification makes clear that optional fields must follow the format TAG:TYPE:VALUE
  Type   Regexp matching                                       VALUE Description
  A     [!-~]                                                  Printable character
  i     [-+]?[0-9]+                                            Signed integer
  f     [-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?                 Single-precision floating number
  Z     [ !-~]*                                                Printable string, including space
  H     ([0-9A-F][0-9A-F])*                                    Byte array in the Hex format10
  B     [cCsSiIf](,[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)+    Integer or numeric array
  
  However, looking at the samtools source code, I noticed this:
  https://github.com/samtools/samtools/blob/develop/sam_view.c#L920-L931
  switch (aux_type) {
      case 'H':
      case 'Z':
          if (kputs(bam_aux2Z(s), linebuf) < 0) return false;
          break;
      case 'i': kputw(bam_aux2i(s), linebuf); break;
      case 'I': kputuw(bam_aux2i(s), linebuf); break;
      case 'A': kputc(bam_aux2A(s), linebuf); break;
      case 'f': kputd(bam_aux2f(s), linebuf); break;
      case 'B': kputs("*** Unhandled aux type ***", linebuf); return false;
      default:  kputs("*** Unknown aux type ***", linebuf); return false;
  }
  
  Questions:
  (1) I have never seen an "Integer or numeric array" of case "B". What does such an tag look like? Is there an example? 
  (2) Why is this currently "*** Unhandled aux type ***"? Was this the case with previous versions of samtools?
  
  user77: 
  An example would be ZC:B:i,271,271,1,0, which is from TMAP. The i part denotes the values held in the array, which are comma-separated.
  That code is only used in samtools fastq, where that tag type isn't output into fastq files.
  
  
original_text: 1770: <p>The SAM file format specification makes clear that optional fields must follow the format <code>TAG:TYPE:VALUE</code></p>
  
  <pre><code>Type   Regexp matching                                       VALUE Description
  A     [!-~]                                                  Printable character
  i     [-+]?[0-9]+                                            Signed integer
  f     [-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?                 Single-precision floating number
  Z     [ !-~]*                                                Printable string, including space
  H     ([0-9A-F][0-9A-F])*                                    Byte array in the Hex format10
  B     [cCsSiIf](,[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)+    Integer or numeric array
  </code></pre>
  
  <p>However, looking at the samtools source code, I noticed this:</p>
  
  <p><a href="https://github.com/samtools/samtools/blob/develop/sam_view.c#L920-L931" rel="nofollow noreferrer">https://github.com/samtools/samtools/blob/develop/sam_view.c#L920-L931</a></p>
  
  <pre><code>switch (aux_type) {
      case 'H':
      case 'Z':
          if (kputs(bam_aux2Z(s), linebuf) &lt; 0) return false;
          break;
      case 'i': kputw(bam_aux2i(s), linebuf); break;
      case 'I': kputuw(bam_aux2i(s), linebuf); break;
      case 'A': kputc(bam_aux2A(s), linebuf); break;
      case 'f': kputd(bam_aux2f(s), linebuf); break;
      case 'B': kputs("*** Unhandled aux type ***", linebuf); return false;
      default:  kputs("*** Unknown aux type ***", linebuf); return false;
  }
  </code></pre>
  
  <p>Questions:</p>
  
  <p>(1) I have never seen an "Integer or numeric array" of <code>case "B"</code>. What does such an tag look like? Is there an example? </p>
  
  <p>(2) Why is this currently <code>"*** Unhandled aux type ***"</code>? Was this the case with previous versions of samtools?</p>
   77: <ol>
  <li>An example would be <code>ZC:B:i,271,271,1,0</code>, which is from TMAP. The <code>i</code> part denotes the values held in the array, which are comma-separated.</li>
  <li>That code is only used in <code>samtools fastq</code>, where that tag type isn't output into fastq files.</li>
  </ol>
  