3,045
edits
Changes
From Genome Analysis Wiki
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For Example:
For Example:
Reference: ACTGAACCTTGGAAACTG
Reference: ACTGAACCTTGGAAACTGCCGGGGACT
Read: ACTGACTG
Read: ACTGACTGAAACCACT
CIGAR: 4M10N4M
CIGAR: 4M10N4M3I2M4D3M
POS: 5
POS: 5
This means it aligns:
This means it aligns:
Reference: ACTGAACCTTGGAAACTG
Reference: ACTGAACCTTGGAAACTG CCGGGGACT
Read: ACTG ACTG
Read: ACTG ACTGAAACC ACT
Adding the position:
Adding the position:
RefPos: 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
RefPos: 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31
Reference: A C T G A A C C T T G G A A A C T G
Reference: A C T G A A C C T T G G A A A C T G C C G G G G A C T
Read: A C T G A C T G
Read: A C T G A C T G A A A C C A C T
Adding the offsets:
Adding the offsets:
RefPos: 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
RefPos: 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31
refOffset: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17
refOffset: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
Reference: A C T G A A C C T T G G A A A C T G
Reference: A C T G A A C C T T G G A A A C T G C C G G G G A C T
Read: A C T G A C T G
Read: A C T G A C T G A A A C C A C T
queryIndex: 0 1 2 3 4 5 6 7
queryIndex: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
The results of a call to getRefOffset for each value passed in (where NA stands for INDEX_NA):
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)
queryIndex: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16(and any value over 16)
Return: 0 1 2 3 14 15 16 17 NA
Return: 0 1 2 3 14 15 16 17 NA NA NA 18 19 24 25 26 NA
The results of a call to getQueryIndex for each value passed in (where NA stands for INDEX_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)
refOffset: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27(and any value over 27)
Return: 0 1 2 3 NA NA NA NA NA NA NA NA NA NA 4 5 6 7 NA
Return: 0 1 2 3 NA NA NA NA NA NA NA NA NA NA 4 5 6 7 11 12 NA NA NA NA 13 14 15 NA
The results of a call to getRefPosition passing in start position 5 (where NA stands for INDEX_NA):
queryIndex: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16(and any value over 16)
Return: 5 6 7 8 19 20 21 22 NA NA NA 23 24 29 30 31 NA
The results of a call to getQueryIndex using refPosition and start position 5 (where NA stands for INDEX_NA):
refPosition:5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32(and any value over 32)
Return: 0 1 2 3 NA NA NA NA NA NA NA NA NA NA 4 5 6 7 11 12 NA NA NA NA 13 14 15 NA
