Description
Return mate-unmapped and position-known flags independently.
Sequence alignments distinguish flag bits, query/reference coordinates, CIGAR operations and scoring conventions. A single flag or length contribution does not establish a complete valid alignment; consuming reference bases differs from consuming query bases or counting a gap penalty.
Return mate-unmapped and position-known flags independently.
When to use this tool
Use SAM Mate Unmapped Position Policy when checking the stated alignment flag, operation, span or gap-scoring convention.
How to use the tool and how it works
- Enter flag, mateReference, matePosition. Use the units and conventions below.
- Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
- Read mateUnmapped, positionKnown. Inspect mateUnmapped, positionKnown before interpreting the associated values.
Return mate-unmapped and position-known flags independently. Require whole flag 0..65535, nonnegative whole matePosition and nonempty mateReference; bit 0x8 marks unmapped, positionKnown requires reference not asterisk and position > 0.1
SAM/BAM defines separate flag, quality and CIGAR conventions. This local operation does not validate a complete alignment record.2
| Input field | Meaning and units | Accepted input |
|---|---|---|
| flag | Flag | Required. Safe integer; minimum 0; maximum 65535. |
| mateReference | Mate Reference | Required. Text; maximum UTF-16 length 8192. |
| matePosition | Mate Position | Required. Safe integer; minimum 0. |
| Output field | Interpretation | Returned shape |
|---|---|---|
| mateUnmapped | Mate Unmapped | Required. Boolean. |
| positionKnown | Position Known | Required. Boolean. |
{
"input": {
"flag": 9,
"mateReference": "*",
"matePosition": 0
},
"output": {
"mateUnmapped": true,
"positionKnown": false
}
}Limitations and assumptions
- Known position may coexist with an unmapped flag; this does not validate a complete SAM alignment or resolve the mate.
- Inputs must satisfy both the field types and the cross-field conditions above. Invalid input causes an error; a successful false flag or documented placeholder is a different result.
- Numeric calculations use binary floating point unless exact decimal-integer arithmetic is explicitly stated. No hidden measurement tolerance or decimal rounding is added; nonfinite or out-of-contract results are rejected. Numeric signed-zero results are exported as zero.
Alternative or Complementary methods
Use a complete SAM/BAM and reference-aware validator or alignment method with explicit clipping, coordinate and scoring policies for full processing.
References
-
Calculation and input contract: bioinformatics/sam-mate-unmapped-position-policy — tool.io
-
SAM/BAM format specification, version 1.6 — SAM/BAM Format Specification Working Group
Similar or alternative tools
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