3,045
edits
Changes
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| QNAME.Length() > 0 and <= 254
| QNAME.Length() > 0 and <= 254
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|style="background-color:red;"|
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|style="background-color:red;"|
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| QNAME does not contain [ \t\n\r]
| QNAME does not contain [ \t\n\r]
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|style="background-color:red;"|
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|style="background-color:red;"|
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| FLAG is an integer [0-9]+
| FLAG is an integer [0-9]+
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|style="background-color:red;"|
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|style="background-color:red;"|
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| FLAG < 2048 (I think) or [0, (2^16)-1]
| FLAG < 2048 (I think) or [0, (2^16)-1]
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|style="background-color:red;"|
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|style="background-color:red;"|
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| RNAME does not contain [ \t\n\r@=]
| RNAME does not contain [ \t\n\r@=]
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|style="background-color:red;"|
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|style="background-color:red;"|
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| POS is an integer [0-9]+
| POS is an integer [0-9]+
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|style="background-color:red;"|
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|style="background-color:red;"|
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| POS is [0, (2^29)-1]
| POS is [0, (2^29)-1]
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|style="background-color:red;"|
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|style="background-color:red;"|
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| MAPQ is an integer [0-9]+
| MAPQ is an integer [0-9]+
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|style="background-color:red;"|
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|style="background-color:red;"|
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| MAPQ is [0, (2^8)-1]
| MAPQ is [0, (2^8)-1]
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|style="background-color:red;"|
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|style="background-color:red;"|
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| <nowiki>CIGAR ([0-9]+[MIDNSHP])+|\*</nowiki>
| <nowiki>CIGAR ([0-9]+[MIDNSHP])+|\*</nowiki>
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|style="background-color:red;"|
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|style="background-color:red;"|
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| 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)
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|style="background-color:red;"|
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|style="background-color:red;"|
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| 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.
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|style="background-color:red;"|
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|style="background-color:red;"|
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| MPOS is an integer [0-9]+
| MPOS is an integer [0-9]+
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|style="background-color:red;"|
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|style="background-color:red;"|
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| MPOS is [0, (2^29)-1]
| MPOS is [0, (2^29)-1]
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|style="background-color:red;"|
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|style="background-color:red;"|
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| ISIZE is an integer -?[0-9]+
| ISIZE is an integer -?[0-9]+
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|style="background-color:red;"|
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|style="background-color:red;"|
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| ISIZE is [-(2^29), 2^29]
| ISIZE is [-(2^29), 2^29]
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|style="background-color:red;"|
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|style="background-color:red;"|
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| <nowiki>SEQ is [acgtnACGTN.=]+|\*</nowiki>
| <nowiki>SEQ is [acgtnACGTN.=]+|\*</nowiki>
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|style="background-color:red;"|
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|style="background-color:red;"|
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| If SEQ is * then QUAL is *
| If SEQ is * then QUAL is *
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|style="background-color:red;"|
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|style="background-color:red;"|
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| <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>
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|style="background-color:red;"|
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|style="background-color:red;"|
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| If QUAL is not “*” it is the same length as SEQ.
| If QUAL is not “*” it is the same length as SEQ.
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|style="background-color:red;"|
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|style="background-color:red;"|
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| TAG is [A-Z][A-Z0-9]
| TAG is [A-Z][A-Z0-9]
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|style="background-color:red;"|
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|style="background-color:red;"|
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| A TAG only appears once per alignment
| A TAG only appears once per alignment
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|style="background-color:red;"|
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|style="background-color:red;"|
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| VTYPE is [AifZH] for SAM and [AcCsSiIfZH]
| VTYPE is [AifZH] for SAM and [AcCsSiIfZH]
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|style="background-color:red;"|
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|style="background-color:red;"|
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| VALUE does NOT contain [\t\n\r]
| VALUE does NOT contain [\t\n\r]
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|style="background-color:red;"|
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|style="background-color:red;"|
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| For VTYPE = “A”, VALUE is a printable character
| For VTYPE = “A”, VALUE is a printable character
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|style="background-color:red;"|
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|style="background-color:red;"|
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| For VTYPE = “i”, VALUE is a signed 32-bit integer.
| For VTYPE = “i”, VALUE is a signed 32-bit integer.
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|style="background-color:red;"|
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|style="background-color:red;"|
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| For VTYPE = “f”, VALUE is a single-precision float.
| For VTYPE = “f”, VALUE is a single-precision float.
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|style="background-color:red;"|
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|style="background-color:red;"|
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| For VTYPE = “Z”, VALUE is a printable string.
| For VTYPE = “Z”, VALUE is a printable string.
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|style="background-color:red;"|
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|style="background-color:red;"|
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| For VTYPE = “H”, VALUE is a Hex string.
| For VTYPE = “H”, VALUE is a Hex string.
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|style="background-color:red;"|
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|style="background-color:red;"|
|}
|}
