fuse-segments

name	fuse-segments
description	Use when you need to merge simple tabular start/end segments into non-overlapping intervals inside EDirect-style pipelines.
disable-model-invocation	true
user-invocable	true

fuse-segments

Quick Start

• Command: printf '10\t20\tx\n18\t25\ty\n40\t35\tz\n' | PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH /home/vimalinx/miniforge3/envs/bio/bin/fuse-segments
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/fuse-segments
• Full reference: See references/help.md for complete documentation

When To Use This Tool

• Normalize start / end pairs where coordinates may be reversed.
• Merge overlapping or directly adjacent segments into larger blocks.
• Compute merged interval length as a final third column for downstream reporting.

Common Patterns

# 1) Fuse simple segments from a tab-delimited stream
printf '10\t20\tx\n18\t25\ty\n40\t35\tz\n' | \
  PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH \
  /home/vimalinx/miniforge3/envs/bio/bin/fuse-segments

10  25  16
35  40  6

# 2) Use as a cleanup step after generating interval tables elsewhere
upstream_command | \
  PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH \
  /home/vimalinx/miniforge3/envs/bio/bin/fuse-segments \
  > fused_segments.tsv

Recommended Workflow

1. Prepare a table whose first two columns are integer segment bounds.
2. Put the EDirect bin directory on PATH so sort-table can be resolved.
3. Pipe the segment table through fuse-segments and capture the merged output.
4. Confirm that reversed coordinates were normalized and that adjacent segments were intentionally collapsed.

Guardrails

• This wrapper requires sibling EDirect helpers, especially sort-table; absolute-path invocation alone is not enough in a shell without the bio env on PATH.
• It prefilters with grep '^[1-9]', so leading whitespace, zero, and non-digit first columns are silently ignored.
• Only the first two columns matter after filtering; any third column is ignored.
• Empty or filtered-away input can still emit the bogus sentinel row 0\t0\t1, so do not treat any output as automatically valid.