Description
Preserve an explicitly supplied FASTQ read pair index and source format.
Sequence formats distinguish coordinate origins, included endpoints, allele separators and identifier grammars. A genomic interbase position differs from a base number, and a parsed optional-field value may still violate its declared type. Local token checks preserve representation without validating a complete file, sequence, reference assembly or biological interpretation.
Preserve an explicitly supplied FASTQ read pair index and source format.
When to use this tool
Use FASTQ Header Pair Index Token when you already have readId, suppliedPairIndex, sourceFormat and need to preserve an explicitly supplied FASTQ read pair index and source format.
How to use the tool and how it works
- Enter readId, suppliedPairIndex, sourceFormat. Use the units and conventions below.
- Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
- Read token. Use the output convention below.
Enter readId, suppliedPairIndex, sourceFormat using the field constraints below. Encode these values, in exactly that order, as a JSON array and return the serialized array as text in token. String values are preserved without trimming or external terminology lookup.1
| Input field | Meaning and units | Accepted input |
|---|---|---|
| readId | Read Id | Required. Text; minimum UTF-16 length 1; maximum UTF-16 length 8192. |
| suppliedPairIndex | Supplied Pair Index | Required. Text; minimum UTF-16 length 1; maximum UTF-16 length 8192. |
| sourceFormat | Source Format | Required. Text; minimum UTF-16 length 1; maximum UTF-16 length 8192. |
| Output field | Interpretation | Returned shape |
|---|---|---|
| token | Token | Required. Text; maximum UTF-16 length 8192. |
{
"input": {
"readId": "READ17",
"suppliedPairIndex": "1",
"sourceFormat": "instrument header"
},
"output": {
"token": "[\"READ17\",\"1\",\"instrument header\"]"
}
}Limitations and assumptions
- The result records supplied values without inferring a header dialect. Sources and asserted relationships are not independently authenticated.
- 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.
Alternative or Complementary methods
Use the complete applicable file specification and a full format validator for conformance. Verify reference assembly, sequence bounds, annotation and database context before interpreting local fields or coordinate transformations.
References
Similar or alternative tools
- Codon Start Stop Source Tag
Record an explicit codon role and genetic-code source.
- FASTA Header Accession Split
Split a supplied FASTA header into accession and description text.