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SAM Validation Criteria (view source)

Revision as of 14:52, 17 March 2010

1,965 bytes added ,  14:52, 17 March 2010
→‎SAM Alignment Validation
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{| 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:red;"|
 
|style="background-color:red;"|
−
|style="background-color:red;"|
+
|style="background-color:red;"|
 +
|style="background-color:red;"|
 +
|style="background-color:red;"|
 
|-
 
|-
 
| QNAME does not contain [ \t\n\r]
 
| QNAME 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;"|
 
|-
 
|-
 
| FLAG is an integer [0-9]+
 
| FLAG is an integer [0-9]+
 +
|style="background-color:red;"|
 +
|style="background-color:red;"|
 
|style="background-color:red;"|
 
|style="background-color:red;"|
 
|style="background-color:red;"|
 
|style="background-color:red;"|
 
|-
 
|-
 
| FLAG < 2048 (I think) or [0, (2^16)-1]
 
| FLAG < 2048 (I think) or [0, (2^16)-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;"|
 
|-
 
|-
 
| RNAME does not contain [ \t\n\r@=]
 
| RNAME 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;"|
 
|-
 
|-
 
| POS is an integer [0-9]+
 
| POS is an integer [0-9]+
 +
|style="background-color:red;"|
 +
|style="background-color:red;"|
 
|style="background-color:red;"|
 
|style="background-color:red;"|
 
|style="background-color:red;"|
 
|style="background-color:red;"|
 
|-
 
|-
 
| POS is [0, (2^29)-1]
 
| POS 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;"|
 
|-
 
|-
 
| MAPQ is an integer [0-9]+
 
| MAPQ is an integer [0-9]+
 +
|style="background-color:red;"|
 +
|style="background-color:red;"|
 
|style="background-color:red;"|
 
|style="background-color:red;"|
 
|style="background-color:red;"|
 
|style="background-color:red;"|
 
|-
 
|-
 
| MAPQ is [0, (2^8)-1]
 
| MAPQ is [0, (2^8)-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;"|
 
|-
 
|-
 
| <nowiki>CIGAR ([0-9]+[MIDNSHP])+|\*</nowiki>
 
| <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;"|
 
|-
 
|-
 
| 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:red;"|
 +
|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:red;"|
 +
|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 is not “*” it is the same length as SEQ.
 +
|style="background-color:red;"|
 +
|style="background-color:red;"|
 
|style="background-color:red;"|
 
|style="background-color:red;"|
 
|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]
 +
|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;"|
 
|-
 
|-
 
| For VTYPE = “H”, VALUE is a Hex string.
 
| For VTYPE = “H”, VALUE is a Hex 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;"|
Line 128: Line 191:  
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.
    
===SAM Questions===
 
===SAM Questions===
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/663"

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