SAM Validation Criteria

SAM Header Validation Rules

TODO

SAM Header

Validation Criteria	Implemented		Tested
	SAM	BAM	SAM	BAM
All Required Fields are set

SAM Alignment Validation

SAM Alignment Record

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]+		N/A: just interpret the bits as an int.		N/A: just interpret the bits as an int.
FLAG is [0, (2^16)-1]		N/A: only a 16 bit field		N/A: only a 16 bit field
RNAME does not contain [ \t\n\r@=]
RNAME is found in an SQ header record if there are any SQs in the header.
Reference Name length does not match specified length.	N/A: reference name length is in BAM format only		N/A: reference name length is in BAM format only
Reference ID is in range of the number of references	N/A: rID is in BAM format only		N/A: rID is in BAM format only
POS is an integer [0-9]+		N/A: just interpret the bits as an int.		N/A: just interpret the bits as an int.
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

SAM Alignment Record

Validation Criteria	Implemented		Tested
	SAM	BAM	SAM	BAM
If specified to check sort order (either based on SO flag or user specifies coordinate or query name).

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???

BamFile Classes

BamFile