Changeset 3211 for trunk/yat/utility/Aligner.h

Timestamp:

May 5, 2014, 8:38:55 AM (9 years ago)

Author:

Peter

Message:

improve docs of CIGAR

File:

• trunk/yat/utility/Aligner.h (modified) (3 diffs)

trunk/yat/utility/Aligner.h

@@ -146 +146 @@
        represented by an array of length 3.
 
+       <table>
+       <tr><td>\c \#define</td><td>value</td><td>char</td><td>type</td>
+       <td>consume ref</td><td>consume query</td></tr>
+       <tr><td>BAM_CMATCH</td>    <td>0</td><td>M</td><td>3</td>
+       <td>\c true</td><td>\c true</td></tr>
+       <tr><td>BAM_CINS</td>      <td>1</td><td>I</td><td>1</td>
+       <td>\c false</td><td>\c true</td></tr>
+       <tr><td>BAM_CDEL</td>      <td>2</td><td>D</td><td>2</td>
+       <td>\c true</td><td>\c false</td></tr>
+       <tr><td>BAM_CREF_SKIP</td> <td>3</td><td>N</td><td>2</td>
+       <td>\c true</td><td>\c false</td></tr>
+       <tr><td>BAM_CSOFT_CLIP</td><td>4</td><td>S</td><td>1</td>
+       <td>\c false</td><td>\c true</td></tr>
+       <tr><td>BAM_CHARD_CLIP</td><td>5</td><td>H</td><td>0</td>
+       <td>\c false</td><td>\c false</td></tr>
+       <tr><td>BAM_CPAD</td>      <td>6</td><td>P</td><td>0</td>
+       <td>\c false</td><td>\c false</td></tr>
+       <tr><td>BAM_CEQUAL</td>    <td>7</td><td>=</td><td>3</td>
+       <td>\c true</td><td>\c true</td></tr>
+       <tr><td>BAM_CDIFF</td>     <td>8</td><td>X</td><td>3</td>
+       <td>\c true</td><td>\c true</td></tr>
+       <tr><td>BAM_CBACK</td>     <td>9</td><td>B</td><td>0</td>
+       <td>\c false</td><td>\c false</td></tr>
+       </table>
+
        \since new in yat 0.12
      */
@@ -157 +182 @@
 
       /**
-         See defines BAM_CIGAR_*
+         See table in class documntation.
 
          \return operation part of element \a i
@@ -165 +190 @@
       /**
          Translate the op(i) to a descriptive character of one of the
-         following "MIDNSHP=XB"
-
-         \return character describing operation
-         i
+         following "MIDNSHP=XB". See table in class documentation.
+
+         \return character describing operation i
        */
       char opchr(size_t i) const;