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C++ Class: CigarRoller

1,593 bytes added, 17:16, 29 July 2010
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| Returns true if the passed in operator is not the same as this operator, false if they are the same.
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== Mapping Between Reference and Read/Query ==
<code>int32_t CigarRoller::getRefOffset(int32_t queryIndex)</code> and <code>int32_t CigarRoller::getQueryIndex(int32_t refOffset)</code> are used to map between the reference and the read.
 
The queryIndex is the index in the read - from 0 to (read length - 1).
The refOffset is the offset into the reference from the starting position of the read.
 
For Example:
Reference: ACTGAACCTTGGAAACTG
Read: ACTGACTG
CIGAR: 4M10N4M
POS: 5
 
This means it aligns:
Reference: ACTGAACCTTGGAAACTG
Read: ACTG ACTG
 
Adding the position:
RefPos: 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
Reference: A C T G A A C C T T G G A A A C T G
Read: A C T G A C T G
 
Adding the offsets:
RefPos: 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
refOffset: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17
Reference: A C T G A A C C T T G G A A A C T G
Read: A C T G A C T G
queryIndex: 0 1 2 3 4 5 6 7
 
The results of a call to getRefOffset for each value passed in (where NA stands for INDEX_NA):
queryIndex: 0 1 2 3 4 5 6 7 8(and any value over 8)
Return: 0 1 2 3 14 15 16 17 NA
 
The results of a call to getQueryIndex for each value passed in (where NA stands for INDEX_NA):
refOffset: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18(and any value over 18)
Return: 0 1 2 3 NA NA NA NA NA NA NA NA NA NA 4 5 6 7 NA

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