ContigJoin Struct Reference

Collaboration diagram for ContigJoin:

[legend]List of all members.

Public Types
enum	{ notDetermined = 2000000000 }
Public Member Functions
	ContigJoin (ContigHitOnRead *pa, ContigHitOnRead *pb, ReadInfo *pReadInfo)
bool	operator< (const ContigJoin &rhs) const
Public Attributes
ContigHitOnRead *	a
ContigHitOnRead *	b
int	gapSize
int	gapSD

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Detailed Description

Definition at line 130 of file OrderOrient.cpp.

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Member Enumeration Documentation

anonymous enum

Enumerator:

notDetermined

Definition at line 132 of file OrderOrient.cpp.

{ notDetermined=2000000000 };

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Constructor & Destructor Documentation

ContigJoin::ContigJoin	(	ContigHitOnRead *	pa,
		ContigHitOnRead *	pb,
		ReadInfo *	pReadInfo
	)			[inline]

Definition at line 136 of file OrderOrient.cpp.

References a, b, ContigHitOnRead::contigNum, contigSizes, gapSD, gapSize, ReadInfo::insertMean, ReadInfo::insertSD, ContigHitOnRead::isForward, and ContigHitOnRead::position.

  {
    if (pa->contigNum<pb->contigNum)
    { 
      a=pa; b=pb;
    }
    else
    { 
      a=pb; b=pa;
    }
    
    int minInsert 
      =  ((a->isForward) 
      ? contigSizes[a->contigNum]-a->position // TBD +1 ?????
      : a->position )
      + ((b->isForward) 
      ? contigSizes[b->contigNum]-b->position // TBD +1 ?????
      : b->position);

    if (minInsert>pReadInfo->insertMean+(3*pReadInfo->insertSD))
    { 
      cout << "WARNING: lower bound for insert=" << minInsert
           << " mean=" << pReadInfo->insertMean
           << " SD=" << pReadInfo->insertSD << endl;
      // TBD throw an exception, catch outside ctor
    }

    gapSize=pReadInfo->insertMean-minInsert;
    gapSD=pReadInfo->insertSD;

    if (gapSize<0)
    {
      cout << "WARNING: estimated gap size=" << gapSize
           << endl;
      //      gapSize=0;
    }
    else cout << "Computed gap size of " << gapSize 
              << ", SD=" << gapSD << endl;


  }

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Member Function Documentation

bool ContigJoin::operator<

(

const ContigJoin &

rhs

)

const [inline]

Definition at line 185 of file OrderOrient.cpp.

References a, b, and ContigHitOnRead::contigNum.

  {
    return (    ( a->contigNum < rhs.a->contigNum )
             || (    ( a->contigNum == rhs.a->contigNum )
                  && ( b->contigNum < rhs.b->contigNum )) ); 
  }

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Member Data Documentation

ContigHitOnRead* ContigJoin::a

Definition at line 180 of file OrderOrient.cpp.

Referenced by ContigJoin(), and operator<().

ContigHitOnRead* ContigJoin::b

Definition at line 181 of file OrderOrient.cpp.

Referenced by ContigJoin(), and operator<().

int ContigJoin::gapSize

Definition at line 182 of file OrderOrient.cpp.

Referenced by ContigJoin().

int ContigJoin::gapSD

Definition at line 183 of file OrderOrient.cpp.

Referenced by ContigJoin().

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The documentation for this struct was generated from the following file:

• EnsemblServer/OrderOrient.cpp

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