3,045
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchno edit summary
'''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
{| class="wikitable" style="width:100%" border="1"
|+ style="font-size:150%"|'''SAM Header'''
! rowspan='2' width="60%"|Validation Criteria
! colspan="2" width="20%"|Implemented
! colspan="2" width="20%"|Tested
|-
! width="10%"|SAM
! width="10%"|BAM
! width="10%"|SAM
! width="10%"|BAM
|-
| All Required Fields are set
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|-
| 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;"|
|-
| 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;"|
|-
| 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;"|
|-
| 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;"|
|-
| 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;"|
|-
| SQ/LN is not a number
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|-
| 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;"|
|-
| 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;"|
|-
| 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;"|
|}
=== SAM Alignment Validation ===
=== SAM Alignment Validation ===
{| class="wikitable" style="width:100%" border="1"
{| class="wikitable" style="width:100%" border="1"
|+ style="font-size:150%"|'''SAM Alignment Record'''
|+ style="font-size:150%"|'''SAM Alignment Record'''
! width="70%"|Validation Criteria
! rowspan='2' width="60%"|Validation Criteria
! width="15%"|Implemented
! colspan="2" width="20%"|Implemented
! width="15%"|Tested
! colspan="2" width="20%"|Tested
|-
! width="10%"|SAM
! width="10%"|BAM
! width="10%"|SAM
! width="10%"|BAM
|-
|-
| QNAME.Length() > 0 and <= 254
| QNAME.Length() > 0 and <= 254
|style="background-color:green;"|
|style="background-color:green;"|
|style="background-color:green;"|
|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:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|-
|-
| FLAG is an integer [0-9]+
| FLAG is an integer [0-9]+
|style="background-color:green;"|
|style="background-color:grey;"| N/A: just interpret the bits as an int.
|style="background-color:green;"|
|style="background-color:grey;"| N/A: just interpret the bits as an int.
|-
| FLAG is [0, (2^16)-1]
|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:green;"|
|style="background-color:grey;"| N/A: only a 16 bit field
|-
| RNAME does not contain [ \t\n\r@=]
|style="background-color:green;"|
|style="background-color:green;"|
|style="background-color:green;"|
|style="background-color:red;"|
|style="background-color:red;"|
|-
| RNAME is found in an SQ header record if there are any SQs in the header.
|style="background-color:green;"|
|style="background-color:green;"|
|style="background-color:green;"|
|style="background-color:red;"|
|style="background-color:red;"|
|-
|-
| FLAG < 2048 (I think) or [0, (2^16)-1]
| Reference Name length does not match specified length.
|style="background-color:grey;"| N/A: reference name length is in BAM format only
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:grey;"| N/A: reference name length is in BAM format only
|style="background-color:red;"|
|style="background-color:red;"|
|-
|-
| RNAME does not contain [ \t\n\r@=]
| Reference ID is in range of the number of references
|style="background-color:grey;"| N/A: rID is in BAM format only
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:grey;"| N/A: rID is in BAM format only
|style="background-color:red;"|
|style="background-color:red;"|
|-
|-
| POS is an integer [0-9]+
| POS is an integer [0-9]+
|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.
|style="background-color:green;"|
|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:green;"|
|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:grey;"| N/A: just interpret the bits as an int.
|style="background-color:green;"|
|style="background-color:grey;"| N/A: just interpret the bits as an int.
|-
| 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
|style="background-color:green;"|
|style="background-color:grey;"| N/A: only a 8 bit field
|-
| <nowiki>CIGAR ([0-9]+[MIDNSHP])+|\*</nowiki>
|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;"|
|-
|-
| <nowiki>CIGAR ([0-9]+[MIDNSHP])+|\*</nowiki>
| CIGAR string matches the length of SEQ if both are not "*"
|style="background-color:red;"|
|style="background-color:green;"|
|style="background-color:green;"|
|style="background-color:green;"|
|style="background-color:red;"|
|style="background-color:red;"|
|-
|-
| MRNM does not contain [ \t\n\r@] ('=' means it is the same as RNAME)
| MRNM does not contain [ \t\n\r@] ('=' means it is the same as RNAME)
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|-
|-
| If SQ is in the header RNAME & MRNM (if not “=”) must be in SQ.
| If SQ is in the header RNAME & MRNM (if not “=”) must be in SQ.
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|-
|-
| MPOS is an integer [0-9]+
| MPOS is an integer [0-9]+
|style="background-color:green;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|-
|-
| MPOS is [0, (2^29)-1]
| MPOS is [0, (2^29)-1]
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|-
|-
| ISIZE is an integer -?[0-9]+
| ISIZE is an integer -?[0-9]+
|style="background-color:green;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|-
|-
| ISIZE is [-(2^29), 2^29]
| ISIZE is [-(2^29), 2^29]
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|-
|-
| <nowiki>SEQ is [acgtnACGTN.=]+|\*</nowiki>
| <nowiki>SEQ is [acgtnACGTN.=]+|\*</nowiki>
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|-
|-
| If SEQ is * then QUAL is *
| If SEQ is * then QUAL is *
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|-
|-
| <nowiki>QUAL is [!-~]+|* → dec 33 – 126 or dec 42 (which is in 32-126) (for BAM, it is between [0,93])</nowiki>
| <nowiki>QUAL is [!-~]+|* → dec 33 – 126 or dec 42 (which is in 32-126) (for BAM, it is between [0,93])</nowiki>
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|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:green;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:green;"|
|style="background-color:red;"|
|style="background-color:red;"|
|-
|-
| TAG is [A-Z][A-Z0-9]
| TAG is [A-Z][A-Z0-9]
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|-
|-
| A TAG only appears once per alignment
| A TAG only appears once per alignment
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|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;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|-
|-
| VALUE does NOT contain [\t\n\r]
| VALUE does NOT contain [\t\n\r]
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|-
|-
| For VTYPE = “A”, VALUE is a printable character
| For VTYPE = “A”, VALUE is a printable character
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|-
|-
| For VTYPE = “i”, VALUE is a signed 32-bit integer.
| For VTYPE = “i”, VALUE is a signed 32-bit integer.
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|-
|-
| For VTYPE = “f”, VALUE is a single-precision float.
| For VTYPE = “f”, VALUE is a single-precision float.
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|-
|-
| For VTYPE = “Z”, VALUE is a printable string.
| For VTYPE = “Z”, VALUE is a printable string.
|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;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|-
| For TAG = E2, 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;"|
|-
| For TAG = E2, each base should be different than the read Base (unless 'N')
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|style="background-color:red;"|
|-
| 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;"|
|-
|}
|}
NOTE: There are other TAG Validations that can be done. They will come later.
NOTE: There are other TAG Validations that can be done. They will come later.
NOTE: There are other BAM 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 ==
{| class="wikitable" style="width:100%" border="1"
|+ style="font-size:150%"|'''SAM Alignment Record'''
! rowspan='2' width="60%"|Validation Criteria
! colspan="2" width="20%"|Implemented
! colspan="2" width="20%"|Tested
|-
! width="10%"|SAM
! width="10%"|BAM
! width="10%"|SAM
! width="10%"|BAM
|-
| If specified to check sort order (either based on SO flag or user specifies coordinate or query name).
|style="background-color:green;"|
|style="background-color:green;"|
|style="background-color:green;"|
|style="background-color:green;"|
|}
===SAM Questions===
===SAM Questions===
**Same question for MRNM = “*” and MPOS & ISIZE = 0
**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???
*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 ==
[[C++ Library: libbam|BamFile]]
