Ignore:
Timestamp:
May 3, 2014, 4:15:32 PM (8 years ago)
Author:
Peter
Message:

improve docs of CIGAR. closes #785

File:
1 edited

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  • trunk/yat/utility/Aligner.h

    r3200 r3203  
    132132
    133133    /**
     134       \brief Compact Idiosyncratic Gapped Alignment Report
     135
     136       A CIGAR is a representation of an alignment, an array of
     137       operation/length where the operation and length is packed into
     138       a uint32_t. So a CIGAR of e.g. '3M1D5M' means alignment is
     139       three matches, one deletion, and five matches, which is
     140       represented by an array of length 3.
     141
    134142       \since new in yat 0.12
    135143     */
     
    143151
    144152      /**
    145          \return operation i
     153         See defines BAM_CIGAR_*
     154
     155         \return operation part of element \a i
    146156       */
    147157      uint8_t op(size_t i) const;
    148158
    149159      /**
    150          \return character describing operation i
     160         Translate the op(i) to a descriptive character of one of the
     161         following "MIDNSHP=XB"
     162
     163         \return character describing operation
     164         i
    151165       */
    152166      char opchr(size_t i) const;
     
    158172
    159173      /**
    160          Erase last operation.
     174         Erase last \a len operation.
    161175       */
    162176      void pop_back(uint32_t len=1);
    163177
    164178      /**
    165          Erase first operation.
     179         Erase first \a len operation.
    166180       */
    167181      void pop_front(uint32_t len=1);
    168182
    169183      /**
    170          Add an operation \a op of length \a len at back of cigar.
     184         Add an operation \a op of length \a len at back of cigar. If
     185         last operation equals \a op, length of that element is
     186         changed and the size() is not modified.
    171187       */
    172188      void push_back(uint8_t op, uint32_t len=1);
     
    178194
    179195      /**
    180          \return cigar element i
    181        */
    182       uint32_t operator[](size_t) const;
     196         \return cigar element \a i
     197       */
     198      uint32_t operator[](size_t i) const;
    183199
    184200      /**
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