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LibStatGen: ASP (view source)

Revision as of 11:45, 30 April 2012

231 bytes added ,  11:45, 30 April 2012
→‎Record Type: Detailed
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| numBases || style="text-align: left;"| Number of bases at this position || uint8_t || 1-255
 
| numBases || style="text-align: left;"| Number of bases at this position || uint8_t || 1-255
 
|-
 
|-
−
| all Bases || style="text-align: left;"| 4-bit encoded bases/deletions for this position
+
| all Bases || style="text-align: left;"| 8-bit encoded bases/deletions for this position
−
1st base is in the upper bits of 1st byte
+
| uint8_t[numBases]
−
 
  −
if odd number of bases, the lower bits of the last byte are 0.
  −
| uint8_t[(numBases+1)/2]
   
| 0=A, 1=C,  
 
| 0=A, 1=C,  
 
2=G, 3=T,
 
2=G, 3=T,
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|-
 
|-
 
| allStrands || style="text-align: left;"| Strand for all bases at this position   
 
| allStrands || style="text-align: left;"| Strand for all bases at this position   
−
strand of the 1st base is in the uppermost bit of the first byte
+
| uint8_t[numBases]
−
 
  −
if numBases is not a multiple of 8, the extra lower bits are set to 0
  −
| uint8_t[(numBases+7)/8]
   
| 0 - forward
 
| 0 - forward
 
1 - reverse
 
1 - reverse
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==== Example ====
 
==== Example ====
   −
Hex dump of a record: 0x0302231d1d0201402c22
+
Hex dump of a record: 0x230202031d1d020100012c22
    
{| style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse; text-align: center;" border="1"  
 
{| style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse; text-align: center;" border="1"  
 
|-style="background: #f2f2f2; text-align: center;"
 
|-style="background: #f2f2f2; text-align: center;"
−
! width="25" | 0 !! width="25" | 1 !! width="25" | 2 !! width="25" | 3 !! width="25" | 4 !! width="25" | 5 !! width="25" | 6 !! width="25" | 7 !! width="25" | 8 !! width="25" | 9 !! width="25" | 10 !! width="25" | 11 !! width="25" |  12 !! width="25" | 13 !! width="25" | 14 !! width="25" | 15 !! width="25" | 16 !! width="25" | 17 !! width="25" | 18 !! width="25" | 19 !! width="25" | 20 !! width="25" | 21 !! width="25" |  22 !! width="25" | 23 !! width="25" | 24 !! width="25" | 25 !! width="25" | 26 !! width="25" | 27 !! width="25" | 28 !! width="25" | 29 !! width="25" | 30 !! width="25" | 31 !! width="25" | 32 !! width="25" | 33 !! width="25" | 34 !! width="25" | 35 !! width="25" | 36 !! width="25" | 37 !! width="25" | 38 !! width="25" | 39 !! width="25" | 40 !! width="25" | 41 !! width="25" |  42 !! width="25" | 43 !! width="25" | 44 !! width="25" | 45 !! width="25" | 46 !! width="25" | 47 !! width="25" | 48 !! width="25" | 49 !! width="25" | 50 !! width="25" | 51 !! width="25" | 52 !! width="25" | 53 !! width="25" | 54 !! width="25" | 55 !! width="25" | 56 !! width="25" | 57 !! width="25" | 58 !! width="25" | 59 !! width="25" | 60 !! width="25" | 61 !! width="25" | 62 !! width="25" | 63 !! width="25" | 64 !! width="25" | 65 !! width="25" | 66 !! width="25" | 67 !! width="25" | 68 !! width="25" | 69 !! width="25" | 70 !! width="25" | 71 !! width="25" | 72 !! width="25" | 73 !! width="25" | 74 !! width="25" | 75 !! width="25" | 76 !! width="25" | 77 !! width="25" | 78 !! width="25" | 79
+
! width="25" | 0 !! width="25" | 1 !! width="25" | 2 !! width="25" | 3 !! width="25" | 4 !! width="25" | 5 !! width="25" | 6 !! width="25" | 7 !! width="25" | 8 !! width="25" | 9 !! width="25" | 10 !! width="25" | 11 !! width="25" |  12 !! width="25" | 13 !! width="25" | 14 !! width="25" | 15 !! width="25" | 16 !! width="25" | 17 !! width="25" | 18 !! width="25" | 19 !! width="25" | 20 !! width="25" | 21 !! width="25" |  22 !! width="25" | 23 !! width="25" | 24 !! width="25" | 25 !! width="25" | 26 !! width="25" | 27 !! width="25" | 28 !! width="25" | 29 !! width="25" | 30 !! width="25" | 31 !! width="25" | 32 !! width="25" | 33 !! width="25" | 34 !! width="25" | 35 !! width="25" | 36 !! width="25" | 37 !! width="25" | 38 !! width="25" | 39 !! width="25" | 40 !! width="25" | 41 !! width="25" |  42 !! width="25" | 43 !! width="25" | 44 !! width="25" | 45 !! width="25" | 46 !! width="25" | 47 !! width="25" | 48 !! width="25" | 49 !! width="25" | 50 !! width="25" | 51 !! width="25" | 52 !! width="25" | 53 !! width="25" | 54 !! width="25" | 55 !! width="25" | 56 !! width="25" | 57 !! width="25" | 58 !! width="25" | 59 !! width="25" | 60 !! width="25" | 61 !! width="25" | 62 !! width="25" | 63 !! width="25" | 64 !! width="25" | 65 !! width="25" | 66 !! width="25" | 67 !! width="25" | 68 !! width="25" | 69 !! width="25" | 70 !! width="25" | 71 !! width="25" | 72 !! width="25" | 73 !! width="25" | 74 !! width="25" | 75 !! width="25" | 76 !! width="25" | 77 !! width="25" | 78 !! width="25" | 79 !! width="25" | 80 !! width="25" | 81 !! width="25" | 82 !! width="25" | 83 !! width="25" | 84 !! width="25" | 85 !! width="25" | 86 !! width="25" | 87 !! width="25" | 88 !! width="25" | 89 !! width="25" | 90 !! width="25" | 91 !! width="25" | 92 !! width="25" | 93 !! width="25" | 94 !! width="25" | 95
 
|-
 
|-
−
| colspan="8" | 23 || colspan="8" | 02 || colspan="8" | 23 || colspan="8" | 1D || colspan="8" | 1D || colspan="8" | 02 || colspan="8" | 01 || colspan="8" | 40 || colspan="8" | 2C || colspan="8" | 22
+
| colspan="8" | 23 || colspan="8" | 02 || colspan="8" | 02 || colspan="8" | 03 || colspan="8" | 1D || colspan="8" | 1D || colspan="8" | 02 || colspan="8" | 01 || colspan="8" | 00 || colspan="8" | 01 || colspan="8" | 2C || colspan="8" | 22
 
|-
 
|-
−
| colspan="4" | RefBase = G || colspan="4" | Type = DETAILED || colspan="8" | NumBases = 2 || colspan="8" | Base1 = 2 = G, Base2 = 3 = T || colspan="8" | Qual1 = 0x1D = 29 = '>'  || colspan="8" | Qual2 = 0x1D = 29 = '>' || colspan="8" | Cycle1 = 2 || colspan="8" | Cycle2 = 1 || colspan="8" | Strand1 (bit 56) = 0 = forward,
+
| colspan="4" | RefBase = G || colspan="4" | Type = DETAILED || colspan="8" | NumBases = 2 || colspan="8" | Base1 = 2 = G || colspan="8" | Base2 = 3 = T || colspan="8" | Qual1 = 0x1D = 29 = '>'  || colspan="8" | Qual2 = 0x1D = 29 = '>' || colspan="8" | Cycle1 = 2 || colspan="8" | Cycle2 = 1 || colspan="8" | Strand1 = 0 = forward || colspan="8" | Strand2 = 1 = reverse || colspan="8" | MapQual1 = 0x2C = 44 || colspan="8" | MapQual2 = 0x22 = 34
−
Strand2 (bit 57) = 1 = reverse,
  −
 
  −
extra bits are dummy bits = 0
  −
| colspan="8" | MapQual1 = 0x2C = 44 || colspan="8" | MapQual2 = 0x22 = 34
   
|-
 
|-
−
| colspan="4" | 2 || colspan="4" | 3 || colspan="4" | 0 || colspan="4" | 2 || colspan="4" | 2 || colspan="4" | 3 || colspan="4" | 1 || colspan="4" | D || colspan="4" | 1 || colspan="4" | D || colspan="4" | 0 || colspan="4" | 2 || colspan="4" | 0 || colspan="4" | 1 || colspan="4" | 4 || colspan="4" | 0 || colspan="4" | 2 || colspan="4" | C || colspan="4" | 2 || colspan="4" | 2
+
| colspan="4" | 2 || colspan="4" | 3 || colspan="4" | 0 || colspan="4" | 2 || colspan="4" | 0 || colspan="4" | 2 || colspan="4" | 0 || colspan="4" | 3 || colspan="4" | 1 || colspan="4" | D || colspan="4" | 1 || colspan="4" | D || colspan="4" | 0 || colspan="4" | 2 || colspan="4" | 0 || colspan="4" | 1 || colspan="4" | 0 || colspan="4" | 0 || colspan="4" | 0 || colspan="4" | 1 || colspan="4" | 2 || colspan="4" | C || colspan="4" | 2 || colspan="4" | 2
 
|-
 
|-
−
| 0 || 0 || 1 || 0 || 0 || 0 || 1 || 1 || 0 || 0 || 0 || 0 || 0 || 0 || 1 || 0 || 0 || 0 || 1 || 0 || 0 || 0 || 1 || 1 || 0 || 0 || 0 || 1 || 1 || 1 || 0 || 1 || 0 || 0 || 0 || 1 || 1 || 1 || 0 || 1 || 0 || 0 || 0 || 0 || 0 || 0 || 1 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 1 || 0 || 1 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 1 || 0 || 1 || 1 || 0 || 0 || 0 || 0 || 1 || 0 || 0 || 0 || 1 || 0
+
| 0 || 0 || 1 || 0 || 0 || 0 || 1 || 1 || 0 || 0 || 0 || 0 || 0 || 0 || 1 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 1 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 1 || 1 || 0 || 0 || 0 || 1 || 1 || 1 || 0 || 1 || 0 || 0 || 0 || 1 || 1 || 1 || 0 || 1 || 0 || 0 || 0 || 0 || 0 || 0 || 1 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 1 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 1 || 0 || 0 || 1 || 0 || 1 || 1 || 0 || 0 || 0 || 0 || 1 || 0 || 0 || 0 || 1 || 0
 
|}
 
|}
  
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/4832"

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