| name | print-missing-subranges |
| description | Use when reporting gaps in an ordered list of ascending integer positions, identifiers, or coordinates by printing the missing ranges between observed values. |
| disable-model-invocation | true |
| user-invocable | true |
print-missing-subranges
Quick Start
- Command:
print-missing-subranges [file ...]
- Local executable:
/home/vimalinx/miniforge3/envs/bio/bin/print-missing-subranges
- I/O shape: reads ordered integers from stdin or files and writes missing ranges such as
3-4
When To Use This Tool
- Find numeric gaps in a sorted one-column list of positions or identifiers.
- Report missing spans between observed values before downstream range filling or QC.
- Keep the logic in a tiny shell pipeline instead of writing custom
awk each time.
- Handle simple integer streams, not BED / GFF interval files.
Common Patterns
printf '1\n2\n5\n8\n' | print-missing-subranges
print-missing-subranges ordered_positions.txt
xtract -pattern DocumentSummary -element Id |
sort -n |
print-missing-subranges
Recommended Workflow
- Reduce the input to one ascending integer per line.
- Sort numerically before calling the wrapper if the source stream is not already ordered.
- Interpret each emitted
start-end row as a missing inclusive block.
- Stop here if you only need gap reporting; use a separate tool if you need interval reconstruction or filling.
Guardrails
- The wrapper assumes ordered ascending integers; unsorted input or duplicates will give misleading ranges.
- There is no real help or version interface, and flags such as
--help are treated as filenames.
- The first expected value is implicitly
1, so an input starting at 5 will report 1-4 as missing.
- The tool only reports gaps between observed values; it does not infer a terminal upper bound after the last line.
- This is a one-column integer gap finder, not a generic genomic interval subtraction tool.
