SAM Validation Criteria - Revision history

Mktrost at 19:51, 27 August 2010

2010-08-27T19:51:57Z

← Older revision		Revision as of 15:51, 27 August 2010
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	\|style="background-color:red;"\|		\|style="background-color:red;"\|
	\|style="background-color:red;"\|		\|style="background-color:red;"\|
			\|-
			\| Header has X-lines or fewer (or a max number of SQ lines (this was a problem once of a file with a crazy number of header lines)
			\|style="background-color:red;"\|
			\|style="background-color:red;"\|
			\|style="background-color:red;"\|
			\|style="background-color:red;"\|
	\|}		\|}

Mktrost at 21:36, 21 July 2010

2010-07-21T21:36:59Z

← Older revision		Revision as of 17:36, 21 July 2010
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			'''NOTE: Not all validation Criteria has been listed here, and not all listed here have been implemented (Implemented checks are marked green.)'''
	NOTE: Not all validation Criteria has been listed here, and not all listed here have been implemented (Implemented checks are marked green.)

	=== SAM Header Validation Rules ===		=== SAM Header Validation Rules ===

Mktrost at 21:36, 21 July 2010

2010-07-21T21:36:43Z

← Older revision		Revision as of 17:36, 21 July 2010
Line 1:		Line 1:

			NOTE: Not all validation Criteria has been listed here, and not all listed here have been implemented (Implemented checks are marked green.)

	=== SAM Header Validation Rules ===		=== SAM Header Validation Rules ===
	TODO		TODO

Mktrost at 21:09, 21 July 2010

2010-07-21T21:09:08Z

← Older revision		Revision as of 17:09, 21 July 2010
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	\|-		\|-
	\| CIGAR string matches the length of SEQ if both are not "*"		\| CIGAR string matches the length of SEQ if both are not "*"
	\|style="background-color:~~red~~;"\|		\|style="background-color:green;"\|
	\|style="background-color:~~red~~;"\|		\|style="background-color:green;"\|
	\|style="background-color:~~red~~;"\|		\|style="background-color:green;"\|
	\|style="background-color:red;"\|		\|style="background-color:red;"\|
	\|-		\|-

Mktrost at 19:37, 21 July 2010

2010-07-21T19:37:21Z

← Older revision		Revision as of 15:37, 21 July 2010
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	\|-		\|-
	\| <nowiki>CIGAR ([0-9]+[MIDNSHP])+\|\*</nowiki>		\| <nowiki>CIGAR ([0-9]+[MIDNSHP])+\|\*</nowiki>
			\|style="background-color:red;"\|
			\|style="background-color:red;"\|
			\|style="background-color:red;"\|
			\|style="background-color:red;"\|
			\|-
			\| CIGAR string matches the length of SEQ if both are not "*"
	\|style="background-color:red;"\|		\|style="background-color:red;"\|
	\|style="background-color:red;"\|		\|style="background-color:red;"\|

Mktrost at 19:35, 21 July 2010

2010-07-21T19:35:12Z

← Older revision		Revision as of 15:35, 21 July 2010
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	\|style="background-color:red;"\|		\|style="background-color:red;"\|
	\|-		\|-
	\| If QUAL is not “*” ~~it is~~ the same length ~~as SEQ~~.		\| If QUAL and SEQ are not “*” they are the same length.
	\|style="background-color:~~red;"\|~~		\|style="background-color:green;"\|
	~~\|style="background-color:red~~;"\|
	\|style="background-color:red;"\|		\|style="background-color:red;"\|
			\|style="background-color:green;"\|
	\|style="background-color:red;"\|		\|style="background-color:red;"\|
	\|-		\|-

Mktrost: /* SAM Alignment Validation */

2010-07-20T16:29:26Z

SAM Alignment Validation

← Older revision		Revision as of 12:29, 20 July 2010
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	\|style="background-color:red;"\|		\|style="background-color:red;"\|
	\|-		\|-
	\| QNAME ~~does not contain~~ [ ~~\t\n\r~~]		\| QNAME is valid: [!-?A-~] (printable characters minus space and '@') '''This is a new regular expression'''
	\|style="background-color:~~green~~;"\|		\|style="background-color:red;"\|
	\|style="background-color:~~green~~;"\|		\|style="background-color:red;"\|
	\|style="background-color:~~green~~;"\|		\|style="background-color:red;"\|
	\|style="background-color:red;"\|		\|style="background-color:red;"\|
	\|-		\|-
Line 300:		Line 300:

	Consider may want to validate the cigar string against the read length...		Consider may want to validate the cigar string against the read length...


	== Other Read Validation ==		== Other Read Validation ==

Mktrost: /* SAM Header Validation Rules */

2010-07-20T16:23:08Z

SAM Header Validation Rules

@@ Line 17: / Line 17: @@
 |style="background-color:red;"|
 |style="background-color:red;"|
 |}

Mktrost at 21:24, 24 May 2010

2010-05-24T21:24:35Z

@@ Line 181: / Line 181: @@
 |style="background-color:red;"|
 |-
-| VTYPE is [AifZH] for SAM and [AcCsSiIfZH]
+| VTYPE is [AifZH] for SAM and [AcCsSiIfZH] for BAM
 |style="background-color:red;"|
 |style="background-color:red;"|
@@ Line 222: / Line 222: @@
 |style="background-color:red;"|
 |style="background-color:red;"|
 |}

Mktrost at 17:04, 21 May 2010

2010-05-21T17:04:28Z

← Older revision		Revision as of 13:04, 21 May 2010
Line 50:		Line 50:
	\|-		\|-
	\| FLAG is [0, (2^16)-1]		\| FLAG is [0, (2^16)-1]
	\|style="background-color:green;"\|		\|style="background-color:green;"\| Parse Error since it will be written into a 16 bit field.
	\|style="background-color:grey;"\| N/A: only a 16 bit field		\|style="background-color:grey;"\| N/A: only a 16 bit field
	\|style="background-color:green;"\|		\|style="background-color:green;"\|
Line 86:		Line 86:
	\|-		\|-
	\| POS is [0, (2^29)-1]		\| POS is [0, (2^29)-1]
	\|style="background-color:green;"\|		\|style="background-color:green;"\| Parse Error if it can't fit in the 32 bit field, other out of range is a validation error.
	\|style="background-color:red;"\|		\|style="background-color:red;"\|
	\|style="background-color:green;"\|		\|style="background-color:green;"\|
Line 93:		Line 93:
	\| MAPQ is an integer [0-9]+		\| MAPQ is an integer [0-9]+
	\|style="background-color:green;"\|		\|style="background-color:green;"\|
	\|style="background-color:~~red~~;"\|		\|style="background-color:grey;"\| N/A: just interpret the bits as an int.
	\|style="background-color:~~red~~;"\|		\|style="background-color:green;"\|
	\|style="background-color:~~red~~;"\|		\|style="background-color:grey;"\| N/A: just interpret the bits as an int.
	\|-		\|-
	\| MAPQ is [0, (2^8)-1]		\| MAPQ is [0, (2^8)-1]
	\|style="background-color:~~red~~;"\|		\|style="background-color:green;"\| Parse Error since it will be written into an 8 bit field.
	\|style="background-color:~~red~~;"\|		\|style="background-color:grey;"\| N/A: only a 8 bit field
	\|style="background-color:~~red~~;"\|		\|style="background-color:green;"\|
	\|style="background-color:~~red~~;"\|		\|style="background-color:grey;"\| N/A: only a 8 bit field
	\|-		\|-
	\| <nowiki>CIGAR ([0-9]+[MIDNSHP])+\|\*</nowiki>		\| <nowiki>CIGAR ([0-9]+[MIDNSHP])+\|\*</nowiki>

← Older revision		Revision as of 13:04, 21 May 2010
Line 50:		Line 50:
	\|-		\|-
	\| FLAG is [0, (2^16)-1]		\| FLAG is [0, (2^16)-1]
	\|style="background-color:green;"\|		\|style="background-color:green;"\| Parse Error since it will be written into a 16 bit field.
	\|style="background-color:grey;"\| N/A: only a 16 bit field		\|style="background-color:grey;"\| N/A: only a 16 bit field
	\|style="background-color:green;"\|		\|style="background-color:green;"\|
Line 86:		Line 86:
	\|-		\|-
	\| POS is [0, (2^29)-1]		\| POS is [0, (2^29)-1]
	\|style="background-color:green;"\|		\|style="background-color:green;"\| Parse Error if it can't fit in the 32 bit field, other out of range is a validation error.
	\|style="background-color:red;"\|		\|style="background-color:red;"\|
	\|style="background-color:green;"\|		\|style="background-color:green;"\|
Line 93:		Line 93:
	\| MAPQ is an integer [0-9]+		\| MAPQ is an integer [0-9]+
	\|style="background-color:green;"\|		\|style="background-color:green;"\|
	\|style="background-color:~~red~~;"\|		\|style="background-color:grey;"\| N/A: just interpret the bits as an int.
	\|style="background-color:~~red~~;"\|		\|style="background-color:green;"\|
	\|style="background-color:~~red~~;"\|		\|style="background-color:grey;"\| N/A: just interpret the bits as an int.
	\|-		\|-
	\| MAPQ is [0, (2^8)-1]		\| MAPQ is [0, (2^8)-1]
	\|style="background-color:~~red~~;"\|		\|style="background-color:green;"\| Parse Error since it will be written into an 8 bit field.
	\|style="background-color:~~red~~;"\|		\|style="background-color:grey;"\| N/A: only a 8 bit field
	\|style="background-color:~~red~~;"\|		\|style="background-color:green;"\|
	\|style="background-color:~~red~~;"\|		\|style="background-color:grey;"\| N/A: only a 8 bit field
	\|-		\|-
	\| <nowiki>CIGAR ([0-9]+[MIDNSHP])+\|\*</nowiki>		\| <nowiki>CIGAR ([0-9]+[MIDNSHP])+\|\*</nowiki>