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SAM Validation Criteria (view source)

Revision as of 15:51, 27 August 2010

3,139 bytes added ,  15:51, 27 August 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.)'''
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=== SAM Header Validation Rules ===
 
=== SAM Header Validation Rules ===
 
TODO
 
TODO
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|-
 
|-
 
| All Required Fields are set
 
| All Required Fields are set
 +
|style="background-color:red;"|
 +
|style="background-color:red;"|
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|style="background-color:red;"|
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|style="background-color:red;"|
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|-
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| If HD line is there, VN is also there.
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|style="background-color:red;"|
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|style="background-color:red;"|
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|style="background-color:red;"|
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|style="background-color:red;"|
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|-
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| HD/VN is not in valid format /^[0-9]+\.[0-9]+$/
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|style="background-color:red;"|
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|style="background-color:red;"|
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|style="background-color:red;"|
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|style="background-color:red;"|
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|-
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| HD/SO is a valid value (unsorted, queryname, coordinate)
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|style="background-color:red;"|
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|style="background-color:red;"|
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|style="background-color:red;"|
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|style="background-color:red;"|
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|-
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| SQ/SN all SQ lines have a unique SN field
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|style="background-color:red;"|
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|style="background-color:red;"|
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|style="background-color:red;"|
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|style="background-color:red;"|
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|-
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| SQ/LN is in the range [1, (2^29) -1]
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|style="background-color:red;"|
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|style="background-color:red;"|
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|style="background-color:red;"|
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|style="background-color:red;"|
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|-
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| SQ/LN is not a number
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|style="background-color:red;"|
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|style="background-color:red;"|
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|style="background-color:red;"|
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|style="background-color:red;"|
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|-
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| RG/ID all RG lines have a unique ID field
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|style="background-color:red;"|
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|style="background-color:red;"|
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|style="background-color:red;"|
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|style="background-color:red;"|
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|-
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| RG/PL is a valid value (ILLUMINA, SOLID, LS454, HELICOS, PACBIO)
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|style="background-color:red;"|
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|style="background-color:red;"|
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|style="background-color:red;"|
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|style="background-color:red;"|
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|-
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| 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;"|
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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;"|
 
|-
 
|-
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|-
 
|-
 
| FLAG is [0, (2^16)-1]
 
| FLAG is [0, (2^16)-1]
−
|style="background-color:green;"|
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|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;"|
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| POS is an integer [0-9]+
 
| POS 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.
 
|-
 
|-
 
| POS is [0, (2^29)-1]
 
| POS is [0, (2^29)-1]
 +
|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:red;"|
+
|style="background-color:green;"|
−
|style="background-color:red;"|
   
|style="background-color:red;"|
 
|style="background-color:red;"|
 
|-
 
|-
 
| 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:green;"| Parse Error since it will be written into an 8 bit field.
 +
|style="background-color:grey;"| N/A: only a 8 bit field
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|style="background-color:green;"|
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|style="background-color:grey;"| N/A: only a 8 bit field
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|-
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| <nowiki>CIGAR ([0-9]+[MIDNSHP])+|\*</nowiki>
 
|style="background-color:red;"|
 
|style="background-color:red;"|
 
|style="background-color:red;"|
 
|style="background-color:red;"|
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|style="background-color:red;"|
 
|style="background-color:red;"|
 
|-
 
|-
−
| <nowiki>CIGAR ([0-9]+[MIDNSHP])+|\*</nowiki>
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| 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;"|
 
|-
 
|-
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|style="background-color:red;"|
 
|style="background-color:red;"|
 
|-
 
|-
−
| If QUAL is not “*” it is the same length as SEQ.
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| 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;"|
 
|-
 
|-
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|style="background-color:red;"|
 
|style="background-color:red;"|
 
|-
 
|-
−
| VTYPE is [AifZH] for SAM and [AcCsSiIfZH]
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| VTYPE is [AifZH] for SAM and [AcCsSiIfZH] for BAM
 
|style="background-color:red;"|
 
|style="background-color:red;"|
 
|style="background-color:red;"|
 
|style="background-color:red;"|
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|style="background-color:red;"|
 
|style="background-color:red;"|
 
|style="background-color:red;"|
 
|style="background-color:red;"|
 +
|-
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| For TAG = E2, length should be the same as the Read Length
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|style="background-color:red;"|
 +
|style="background-color:red;"|
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|style="background-color:red;"|
 +
|style="background-color:red;"|
 +
|-
 +
| For TAG = E2, each base should be different than the read Base (unless 'N')
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|style="background-color:red;"|
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|style="background-color:red;"|
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|style="background-color:red;"|
 +
|style="background-color:red;"|
 +
|-
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| For TAG = U2, length should be the same as the Read Length
 +
|style="background-color:red;"|
 +
|style="background-color:red;"|
 +
|style="background-color:red;"|
 +
|style="background-color:red;"|
 +
|-
 
|}
 
|}
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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 ==
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/1372...1946"

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