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CIGAR Soft Clip Length Tool

Sum S operation lengths in a supplied CIGAR operation stream; alignment-level clipping placement checks are separate.

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Description

Sum soft-clipped CIGAR lengths.

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.

Sum soft-clipped CIGAR lengths.

When to use this tool

Use CIGAR Soft Clip Length when checking the stated alignment flag, operation, span or gap-scoring convention.

How to use the tool and how it works

  1. Enter cigar. Use the units and conventions below.
  2. Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
  3. Read softClipped. Use the output convention below.

Sum soft-clipped CIGAR lengths. Require positive integer length/operation tokens using M/I/D/N/S/H/P/=/X; parse each safe whole length and sum only S operations.1

SAM/BAM defines separate flag, quality and CIGAR conventions. This local operation does not validate a complete alignment record.2

Input fieldMeaning and unitsAccepted input
cigarCigarRequired. Text; maximum UTF-16 length 8192.
Output fieldInterpretationReturned shape
softClippedSoft ClippedRequired. Safe integer.
json
{
  "input": {
    "cigar": "3S6M1P1I4M"
  },
  "output": {
    "softClipped": 3
  }
}

Limitations and assumptions

  • Placement rules for clipping are not validated; the tool does not check a complete SAM record or infer read sequence length.
  • 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 a complete SAM/BAM and reference-aware validator or alignment method with explicit clipping, coordinate and scoring policies for full processing.

References

  1. Calculation and input contract: bioinformatics/cigar-soft-clip-length — tool.io

  2. SAM/BAM format specification, version 1.6 — SAM/BAM Format Specification Working Group

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