gm2ranges

name	gm2ranges
description	Use when converting BLAST/genomic-map alignment summaries into compact strand-and-range tables for later interval fusion.
disable-model-invocation	true
user-invocable	true

gm2ranges

Quick Start

• Command: printf 'acc1 score 1|10 5|3 plus|minus\n' | /home/vimalinx/miniforge3/envs/bio/bin/gm2ranges
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/gm2ranges
• Full reference: See references/help.md for complete usage details

When To Use This Tool

• Turn pipe-delimited start/span/strand alignment summaries into comma-joined genomic ranges.
• Prepare interval strings for downstream helpers such as fuse-ranges.
• Collapse per-hit dense segment fields into one summarized row with a segment count and an overall strand label.

Common Patterns

# 1) Convert one row of starts/spans/strands into a compact range summary
printf 'acc1 score 1|10 5|3 plus|minus\n' | \
  /home/vimalinx/miniforge3/envs/bio/bin/gm2ranges

# 2) Use in the intended EDirect map pipeline
cat smear.asn | \
  blst2gm | \
  /home/vimalinx/miniforge3/envs/bio/bin/gm2ranges | \
  grep minus | \
  cut -f 2-

Recommended Workflow

1. Start from rows that already contain accession, score, start-list, span-list, and strand-list columns.
2. Run gm2ranges as a stdin-to-stdout transformer.
3. Inspect the emitted segment count, aggregate strand label, and comma-joined range list.
4. Feed the range list into downstream normalization or fusion steps if you need canonical interval coordinates.

Guardrails

• The wrapper expects at least five whitespace-delimited columns; shorter rows are silently skipped.
• Minus-strand segments are emitted as descending stop..start strings (for example 12..10), so further normalization is usually needed.
• The aggregate strand label becomes mixed when both plus and minus segments appear in the same row.
• There is no built-in help or version mode.