Difference between revisions of "SAM Validation Criteria"
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Revision as of 14:47, 22 March 2010
SAM Header Validation Rules
TODO
SAM Alignment Validation
| Validation Criteria | Implemented | Tested | ||
|---|---|---|---|---|
| SAM | BAM | SAM | BAM | |
| QNAME.Length() > 0 and <= 254 | ||||
| QNAME does not contain [ \t\n\r] | ||||
| FLAG is an integer [0-9]+ | ||||
| FLAG < 2048 (I think) or [0, (2^16)-1] | ||||
| RNAME does not contain [ \t\n\r@=] | ||||
| POS is an integer [0-9]+ | ||||
| POS is [0, (2^29)-1] | ||||
| MAPQ is an integer [0-9]+ | ||||
| MAPQ is [0, (2^8)-1] | ||||
| CIGAR ([0-9]+[MIDNSHP])+|\* | ||||
| MRNM does not contain [ \t\n\r@] ('=' means it is the same as RNAME) | ||||
| If SQ is in the header RNAME & MRNM (if not “=”) must be in SQ. | ||||
| MPOS is an integer [0-9]+ | ||||
| MPOS is [0, (2^29)-1] | ||||
| ISIZE is an integer -?[0-9]+ | ||||
| ISIZE is [-(2^29), 2^29] | ||||
| SEQ is [acgtnACGTN.=]+|\* | ||||
| If SEQ is * then QUAL is * | ||||
| QUAL is [!-~]+|* → dec 33 – 126 or dec 42 (which is in 32-126) (for BAM, it is between [0,93]) | ||||
| If QUAL is not “*” it is the same length as SEQ. | ||||
| TAG is [A-Z][A-Z0-9] | ||||
| A TAG only appears once per alignment | ||||
| VTYPE is [AifZH] for SAM and [AcCsSiIfZH] | ||||
| VALUE does NOT contain [\t\n\r] | ||||
| For VTYPE = “A”, VALUE is a printable character | ||||
| For VTYPE = “i”, VALUE is a signed 32-bit integer. | ||||
| For VTYPE = “f”, VALUE is a single-precision float. | ||||
| For VTYPE = “Z”, VALUE is a printable string. | ||||
| For VTYPE = “H”, VALUE is a Hex string. | ||||
NOTE: There are other TAG Validations that can be done. They will come later.
NOTE: There may be other BAM Validations that can be done. They will come later.
Consider may want to validate the cigar string against the read length...
Other Read Validation
| Validation Criteria | Implemented | Tested | ||
|---|---|---|---|---|
| SAM | BAM | SAM | BAM | |
| If SO flag is set in the header, fail if the file is not sorted. | ||||
SAM Questions
- Comment says: “If the mapping position of the query is not available, RNAME and CIGAR are set as “*”, and POS and MAPQ as 0.” Is it all or nothing? Can some be set to “*”/0 but not all?
- Same question for MRNM = “*” and MPOS & ISIZE = 0
- Comment says: “The name of a pair/read is required to be unique in the SAM file, but one pair/read may appear multiple times in different alignment records, representing multiple or split hits.” - Is there anything here that needs to be validated???
