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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.)'''
=== 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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| If HD line is there, VN is also there.
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
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| HD/VN is not in valid format /^[0-9]+\.[0-9]+$/
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
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| HD/SO is a valid value (unsorted, queryname, coordinate)
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
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| SQ/SN all SQ lines have a unique SN field
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
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| SQ/LN is in the range [1, (2^29) -1]
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
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| SQ/LN is not a number
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
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| RG/ID all RG lines have a unique ID field
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
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| RG/PL is a valid value (ILLUMINA, SOLID, LS454, HELICOS, PACBIO)
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
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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;"|
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|style="background-color:red;"|
|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;"|
|-
|-
|style="background-color:red;"|
|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:green;"|
|style="background-color:green;"|
|style="background-color:green;"|
|style="background-color:red;"|
|style="background-color:red;"|
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|-
|style="background-color:red;"|
|style="background-color:red;"|
|-
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| 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:green;"|
|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 ==
