Changeset 3211


Ignore:
Timestamp:
May 5, 2014, 8:38:55 AM (7 years ago)
Author:
Peter
Message:

improve docs of CIGAR

File:
1 edited

Legend:

Unmodified
Added
Removed
  • trunk/yat/utility/Aligner.h

    r3207 r3211  
    146146       represented by an array of length 3.
    147147
     148       <table>
     149       <tr><td>\c \#define</td><td>value</td><td>char</td><td>type</td>
     150       <td>consume ref</td><td>consume query</td></tr>
     151       <tr><td>BAM_CMATCH</td>    <td>0</td><td>M</td><td>3</td>
     152       <td>\c true</td><td>\c true</td></tr>
     153       <tr><td>BAM_CINS</td>      <td>1</td><td>I</td><td>1</td>
     154       <td>\c false</td><td>\c true</td></tr>
     155       <tr><td>BAM_CDEL</td>      <td>2</td><td>D</td><td>2</td>
     156       <td>\c true</td><td>\c false</td></tr>
     157       <tr><td>BAM_CREF_SKIP</td> <td>3</td><td>N</td><td>2</td>
     158       <td>\c true</td><td>\c false</td></tr>
     159       <tr><td>BAM_CSOFT_CLIP</td><td>4</td><td>S</td><td>1</td>
     160       <td>\c false</td><td>\c true</td></tr>
     161       <tr><td>BAM_CHARD_CLIP</td><td>5</td><td>H</td><td>0</td>
     162       <td>\c false</td><td>\c false</td></tr>
     163       <tr><td>BAM_CPAD</td>      <td>6</td><td>P</td><td>0</td>
     164       <td>\c false</td><td>\c false</td></tr>
     165       <tr><td>BAM_CEQUAL</td>    <td>7</td><td>=</td><td>3</td>
     166       <td>\c true</td><td>\c true</td></tr>
     167       <tr><td>BAM_CDIFF</td>     <td>8</td><td>X</td><td>3</td>
     168       <td>\c true</td><td>\c true</td></tr>
     169       <tr><td>BAM_CBACK</td>     <td>9</td><td>B</td><td>0</td>
     170       <td>\c false</td><td>\c false</td></tr>
     171       </table>
     172
    148173       \since new in yat 0.12
    149174     */
     
    157182
    158183      /**
    159          See defines BAM_CIGAR_*
     184         See table in class documntation.
    160185
    161186         \return operation part of element \a i
     
    165190      /**
    166191         Translate the op(i) to a descriptive character of one of the
    167          following "MIDNSHP=XB"
    168 
    169          \return character describing operation
    170          i
     192         following "MIDNSHP=XB". See table in class documentation.
     193
     194         \return character describing operation i
    171195       */
    172196      char opchr(size_t i) const;
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