LibStatGen: ASP - Revision history

Mktrost: /* Record Type: Detailed */

2012-04-30T15:45:11Z

Record Type: Detailed

← Older revision		Revision as of 11:45, 30 April 2012
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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
	\|}		\|}

Mktrost: /* Detailed Record Methods */

2012-04-26T19:29:11Z

Detailed Record Methods

← Older revision		Revision as of 15:29, 26 April 2012
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	==== Detailed Record Methods ====		==== Detailed Record Methods ====
	Detailed records contain the number of bases at this position and all of the bases, qualities, cycles, ~~strandss~~, and MQs.		Detailed records contain the number of bases at this position and all of the bases, qualities, cycles, strands, and MQs.

	* <code>getNumBases()</code> returns the number of bases at this position		* <code>getNumBases()</code> returns the number of bases at this position

Mktrost: /* ASP File Format */

2012-04-16T15:17:20Z

ASP File Format

← Older revision		Revision as of 11:17, 16 April 2012
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	The header contains a list of all the read names in the file in the order in which they appear.		The header contains a list of all the read names in the file in the order in which they appear.

	Every record starts with a 1-byte field ~~that indicates~~ the type.		Every record starts with a 1-byte field. The lower 4 bits indicate the type and for some types, the upper four bits indicate the reference base.

	{\| style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"		{\| style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
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	The position associated with a Reference Only record is 1 greater than the position of the previous record unless the previous record is a position record.		The position associated with a Reference Only record is 1 greater than the position of the previous record unless the previous record is a position record.

			The upper 4 bits of the first byte contain the reference base.

	{\| 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"
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	! Field !! Description !! Type !! Value/Range		! Field !! Description !! Type !! Value/Range
	\|-		\|-
	\| type \|\| Reference Only Record Type \|\| ~~uint8_t~~ \|\| 2		\| refBase \|\| Reference Base \|\| 4 bits \|\| 0=A, 1=C, 2=G, 3=T, 4=N
			\|-
			\| type \|\| Reference Only Record Type \|\| 4 bits \|\| 2
	\|-		\|-
	\| numBases \|\| Number of bases at this position \|\| uint8_t \|\| 1-255		\| numBases \|\| Number of bases at this position \|\| uint8_t \|\| 1-255
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	The position associated with a Detailed record is 1 greater than the position of the previous record unless the previous record is a position record.		The position associated with a Detailed record is 1 greater than the position of the previous record unless the previous record is a position record.

			The upper 4 bits of the first byte contain the reference base.

	When a a deletion occurs at a specified position, it counts as a mismatch to the reference.		When a a deletion occurs at a specified position, it counts as a mismatch to the reference.
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	! Field !! Description !! Type !! Value/Range		! Field !! Description !! Type !! Value/Range
	\|-		\|-
	\| type \|\| style="text-align: left;"\| Detailed Record Type \|\| ~~uint8_t~~ \|\| 2		\| refBase \|\| Reference Base \|\| 4 bits \|\| 0=A, 1=C, 2=G, 3=T, 4=N
			\|-
			\| type \|\| style="text-align: left;"\| Detailed Record Type \|\| 4 bits \|\| 3
	\|-		\|-
	\| 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
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	! 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
	\|-		\|-
	\| colspan="8" \| 03 \|\| 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" \| 23 \|\| colspan="8" \| 1D \|\| colspan="8" \| 1D \|\| colspan="8" \| 02 \|\| colspan="8" \| 01 \|\| colspan="8" \| 40 \|\| colspan="8" \| 2C \|\| colspan="8" \| 22
	\|-		\|-
	\| colspan="8" \| 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, 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,
	Strand2 (bit 57) = 1 = reverse,		Strand2 (bit 57) = 1 = reverse,

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	\| colspan="8" \| MapQual1 = 0x2C = 44 \|\| colspan="8" \| MapQual2 = 0x22 = 34		\| colspan="8" \| MapQual1 = 0x2C = 44 \|\| colspan="8" \| MapQual2 = 0x22 = 34
	\|-		\|-
	\| colspan="4" \| 0 \|\| 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" \| 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
	\|-		\|-
	\| 0 \|\| 0 \|\| 0 \|\| 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 \|\| 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
	\|}		\|}


	== API for Reading ASP Files ==		== API for Reading ASP Files ==

Mktrost: /* Reference Only Record Methods */

2012-04-16T15:08:18Z

Reference Only Record Methods

← Older revision		Revision as of 11:08, 16 April 2012
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	* <code>getGLH()</code> returns the GLH of this position		* <code>getGLH()</code> returns the GLH of this position
	* <code>getGLA()</code> returns the GLA of this position		* <code>getGLA()</code> returns the GLA of this position
	* <code>getLikelihood(char base1, char base2~~, char refBase~~)</code> returns the likelihood of this position for the specified genotype.		* <code>getLikelihood(char base1, char base2)</code> returns the likelihood of this position for the specified genotype.
	** When both bases match the reference base, 0 is returned.		** When both bases match the reference base, 0 is returned.
	** If only one of the bases matches the reference base, the GLH is returned.		** If only one of the bases matches the reference base, the GLH is returned.

Mktrost: /* Detailed Record Methods */

2012-04-16T15:08:06Z

Detailed Record Methods

← Older revision		Revision as of 11:08, 16 April 2012
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	* <code>getNumBases()</code> returns the number of bases at this position		* <code>getNumBases()</code> returns the number of bases at this position
	* <code>getRefBase()</code> returns the reference base of this position		* <code>getRefBase()</code> returns the reference base of this position
	* <code>getLikelihood(char base1, char base2~~, char refBase~~)</code> returns the likelihood of this position for the specified genotype.		* <code>getLikelihood(char base1, char base2)</code> returns the likelihood of this position for the specified genotype.
	* <code>getBaseChar(int index)</code> returns the base as a character (A,C,T,G,D,N) in the record at the specified index. The index starts at 0 and goes to numBases - 1. An out of range index returns 'N'. 'D' represents a deletion at this position.		* <code>getBaseChar(int index)</code> returns the base as a character (A,C,T,G,D,N) in the record at the specified index. The index starts at 0 and goes to numBases - 1. An out of range index returns 'N'. 'D' represents a deletion at this position.
	* <code>getPhredQual(int index)</code> returns the phred quality at the specified index. The index starts at 0 and goes to numBases - 1. An out of range index returns -1. An unknown quality and the quality for a deletion is -1.		* <code>getPhredQual(int index)</code> returns the phred quality at the specified index. The index starts at 0 and goes to numBases - 1. An out of range index returns -1. An unknown quality and the quality for a deletion is -1.

Mktrost: /* Advancing to a specific position */

2012-04-16T15:04:09Z

Advancing to a specific position

← Older revision		Revision as of 11:04, 16 April 2012
Line 263:		Line 263:
	<code>getRecord(const char chromName, int32_t pos0Based)</code> returns a reference to the reference-only record at the specified position. The default if that position is not found or has already been passed is to return a reference to an EMPTY record. The returned record is only valid until the next time a new position is read.		<code>getRecord(const char chromName, int32_t pos0Based)</code> returns a reference to the reference-only record at the specified position. The default if that position is not found or has already been passed is to return a reference to an EMPTY record. The returned record is only valid until the next time a new position is read.
	<code>getRefOnlyRecord(const char chromName, int32_t pos0Based)</code> returns a reference to the reference-only record at the specified position. The default if that position is not found, has already been passed, or is not a reference-only record is to return a reference to an EMPTY record. The returned record is only valid until the next time a new position is read.		<code>getRefOnlyRecord(const char chromName, int32_t pos0Based)</code> returns a reference to the reference-only record at the specified position. The default if that position is not found, has already been passed, or is not a reference-only record is to return a reference to an EMPTY record. The returned record is only valid until the next time a new position is read.
	<code>~~getRefOnlyRecord~~(const char chromName, int32_t pos0Based)</code> returns a reference to the detailed record at the specified position. The default if that position is not found, has already been passed, or is not a detailed record is to return a reference to an EMPTY record. The returned record is only valid until the next time a new position is read.		<code>getDetailedRecord(const char chromName, int32_t pos0Based)</code> returns a reference to the detailed record at the specified position. The default if that position is not found, has already been passed, or is not a detailed record is to return a reference to an EMPTY record. The returned record is only valid until the next time a new position is read.
	<code>getLikelihood(const char chromName, int32_t pos0Based, char base1, char base2)</code> returns the likelihood at the specified position of the genotype with the 2 specified ases. The default if that position is not found, has already been passed, or is not a data record is to return a 0.		<code>getLikelihood(const char chromName, int32_t pos0Based, char base1, char base2)</code> returns the likelihood at the specified position of the genotype with the 2 specified ases. The default if that position is not found, has already been passed, or is not a data record is to return a 0.
	<code>getNumBases(const char chromName, int32_t pos0Based)</code> returns the number of bases at the specified position. The default if that position is not found, has already been passed, or is not a data record is to return a 0.		<code>getNumBases(const char chromName, int32_t pos0Based)</code> returns the number of bases at the specified position. The default if that position is not found, has already been passed, or is not a data record is to return a 0.


	==== Determining if EOF reached ====		==== Determining if EOF reached ====

Mktrost: /* API for Reading ASP Files */

2012-04-16T14:59:00Z

API for Reading ASP Files

@@ Line 201: / Line 201: @@
 ==== Reading the ASP Record ====
 Once the file is open, there are two methods to get the next record, <code>getNextRecord</code> and <code>getNextDataRecord</code>.
@@ Line 228: / Line 233: @@
+         }
          // Done reading the file.
 </source>
@@ Line 254: / Line 301: @@
 * <code>getNumBases()</code> returns the number of bases at this position
 * <code>getGLH()</code> returns the GLH of this position
 * <code>getGLA()</code> returns the GLA of this position
@@ Line 265: / Line 313: @@
 * <code>getNumBases()</code> returns the number of bases at this position
 * <code>getLikelihood(char base1, char base2, char refBase)</code> returns the likelihood of this position for the specified genotype.
 * <code>getBaseChar(int index)</code> returns the base as a character (A,C,T,G,D,N) in the record at the specified index.  The index starts at 0 and goes to numBases - 1.  An out of range index returns 'N'.  'D' represents a deletion at this position.

Mktrost: add header

2012-03-21T13:47:59Z

add header

← Older revision		Revision as of 09:47, 21 March 2012
Line 12:		Line 12:
	== ASP File Format ==		== ASP File Format ==

	ASP files are binary files consisting of 4 types of records. Every record starts with a 1-byte field that indicates the type.		ASP files are binary files consisting of a header and 4 types of records.

			The header contains a list of all the read names in the file in the order in which they appear.

			Every record starts with a 1-byte field that indicates the type.

	{\| style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"		{\| style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
Line 20:		Line 24:
	\| 0 \|\| [[#Record Type: Empty\|Empty]] \|\| indicates there are no bases for this position.		\| 0 \|\| [[#Record Type: Empty\|Empty]] \|\| indicates there are no bases for this position.
	\|-		\|-
	\| 1 \|\| [[#Record Type: Position Only\|Position Only]] \|\| specifies the chromsome id/0-based position of the next record (other records do not contain a position).		\| 1 \|\| [[#Record Type: Position Only\|Position Only]] \|\| specifies the chromsome id (see [[#ASP Header\|ASP Header]]) and 0-based position of the next record (other records do not contain a position).
	\|-		\|-
	\| 2 \|\| [[#Record Type: Reference Only\|Reference Only]] \|\| indicates that all bases at this position match the reference and provides the number of bases, GLH, and GLA.		\| 2 \|\| [[#Record Type: Reference Only\|Reference Only]] \|\| indicates that all bases at this position match the reference and provides the number of bases, GLH, and GLA.
Line 30:		Line 34:

	The first record in a file must be a Position Only Record.		The first record in a file must be a Position Only Record.

			=== ASP Header ===

			The chromosome ID found in the [[#Record Type: Position Only\|Position Only records]] is the index into this list starting at 0 and going to length of list - 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;"
			! colspan="2" \| Field !! Description !! Type
			\|-
			\| colspan="2"\| numChroms \|\| The number of chromosomes in the following list \|\| uint32_t
			\|-
			\| colspan="4"\| ''List of chromosome information (numChroms sets of entries)''
			\|-
			\| style="width: 20px"\| \|\| chromNameLen \|\| Length of the chromosome name + 1 (including NULL) \|\| uint32_t
			\|-
			\| \|\| chromName \|\| Chromosome name, NULL terminated \|\| char[chromNameLen]
			\|}

Mktrost at 16:13, 27 January 2012

2012-01-27T16:13:54Z

← Older revision		Revision as of 12:13, 27 January 2012
Line 6:		Line 6:

	Asymmetric Pileup (ASP) is a new pileup file format that we created to replace GLF.		Asymmetric Pileup (ASP) is a new pileup file format that we created to replace GLF.

			<span style="color:#D2691E">'''It is currently in initial test phase, and is not yet available for public use.'''</span>


	== ASP File Format ==		== ASP File Format ==

Mktrost at 15:45, 27 January 2012

2012-01-27T15:45:55Z

@@ Line 92: / Line 92: @@
 The position associated with a Detailed record is 1 greater than the position of the previous record unless the previous record is a position record.
 {| style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse; text-align: center;" border="1"
@@ Line 112: / Line 113: @@
 |-
 | allQuals || style="text-align: left;"| All Phred Quals for this position  || uint8_t[numBases] || 0-254
-- unknown quality
+- unknown quality, deletion qual
 |-
-| allCycles || style="text-align: left;"| 0-based position in the reads for all bases at this position  || uint8_t[numBases] || 0-255
+| allCycles || style="text-align: left;"| 0-based position in the reads for all bases at this position  || uint8_t[numBases] || 0-254, 255 for a deletion
 |-
 | allStrands || style="text-align: left;"| Strand for all bases at this position
@@ Line 225: / Line 226: @@
 Regardless of the record type, <code>getPosition()</code> returns the 0-based position associated with this record.
-''' More AspRecord Methods coming soon!'''
+==== Reference Only Record Methods ====

← Older revision		Revision as of 11:04, 16 April 2012
Line 263:		Line 263:
	<code>getRecord(const char chromName, int32_t pos0Based)</code> returns a reference to the reference-only record at the specified position. The default if that position is not found or has already been passed is to return a reference to an EMPTY record. The returned record is only valid until the next time a new position is read.		<code>getRecord(const char chromName, int32_t pos0Based)</code> returns a reference to the reference-only record at the specified position. The default if that position is not found or has already been passed is to return a reference to an EMPTY record. The returned record is only valid until the next time a new position is read.
	<code>getRefOnlyRecord(const char chromName, int32_t pos0Based)</code> returns a reference to the reference-only record at the specified position. The default if that position is not found, has already been passed, or is not a reference-only record is to return a reference to an EMPTY record. The returned record is only valid until the next time a new position is read.		<code>getRefOnlyRecord(const char chromName, int32_t pos0Based)</code> returns a reference to the reference-only record at the specified position. The default if that position is not found, has already been passed, or is not a reference-only record is to return a reference to an EMPTY record. The returned record is only valid until the next time a new position is read.
	<code>~~getRefOnlyRecord~~(const char chromName, int32_t pos0Based)</code> returns a reference to the detailed record at the specified position. The default if that position is not found, has already been passed, or is not a detailed record is to return a reference to an EMPTY record. The returned record is only valid until the next time a new position is read.		<code>getDetailedRecord(const char chromName, int32_t pos0Based)</code> returns a reference to the detailed record at the specified position. The default if that position is not found, has already been passed, or is not a detailed record is to return a reference to an EMPTY record. The returned record is only valid until the next time a new position is read.
	<code>getLikelihood(const char chromName, int32_t pos0Based, char base1, char base2)</code> returns the likelihood at the specified position of the genotype with the 2 specified ases. The default if that position is not found, has already been passed, or is not a data record is to return a 0.		<code>getLikelihood(const char chromName, int32_t pos0Based, char base1, char base2)</code> returns the likelihood at the specified position of the genotype with the 2 specified ases. The default if that position is not found, has already been passed, or is not a data record is to return a 0.
	<code>getNumBases(const char chromName, int32_t pos0Based)</code> returns the number of bases at the specified position. The default if that position is not found, has already been passed, or is not a data record is to return a 0.		<code>getNumBases(const char chromName, int32_t pos0Based)</code> returns the number of bases at the specified position. The default if that position is not found, has already been passed, or is not a data record is to return a 0.


	==== Determining if EOF reached ====		==== Determining if EOF reached ====