zoom2sam-pl

name	zoom2sam-pl
description	Use when converting legacy Zoom aligner output into SAM and the read length must be supplied explicitly.
disable-model-invocation	true
user-invocable	true

zoom2sam-pl

Quick Start

• Command: zoom2sam.pl [-p] <readLen> alignments.zoom > alignments.sam
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/zoom2sam.pl
• Reference: See references/help.md

When To Use This Tool

• Convert legacy Zoom aligner output into SAM.
• Supply the read length explicitly because the Zoom format handled here does not carry full SAM-ready sequence context.
• Interpret mate relationships with -p when the Zoom output represents paired-end reads.
• Bridge older Illumina/Zoom alignment reports into downstream SAM/BAM tooling.

Common Patterns

# 1) Convert single-end Zoom output with known read length
zoom2sam.pl \
  76 \
  alignments.zoom > alignments.sam

# 2) Convert paired-end Zoom output
zoom2sam.pl \
  -p \
  100 \
  paired.zoom > paired.sam

# 3) Convert and then inspect the SAM body
zoom2sam.pl \
  50 \
  alignments.zoom > alignments.sam
head alignments.sam

Recommended Workflow

1. Confirm the input is the default Illumina-style Zoom output expected by the script.
2. Determine the true read length before conversion and pass it as the first positional argument.
3. Add -p only for paired-end layouts that still preserve mate adjacency.
4. Inspect a few converted records before downstream use, especially because sequence and quality fields are not recovered from the Zoom input.

Guardrails

• The script requires readLen as a positional argument; there is no automatic inference from the input file.
• It explicitly warns that it only supports the default Illumina outputs for Zoom.
• Converted SAM records use * for sequence and quality fields, so this is not suitable when downstream tools require real SEQ and QUAL values.
• Help comes from Perl Getopt::Std, so --help works generically but -help is the wrong pattern for this script family.