soap2sam-pl

name	soap2sam-pl
description	Use when converting legacy SOAP aligner text output into SAM, including paired-end interpretation with `-p`.
disable-model-invocation	true
user-invocable	true

soap2sam-pl

Quick Start

• Command: soap2sam.pl [-p] alignments.soap > alignments.sam
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/soap2sam.pl
• Reference: See references/help.md

When To Use This Tool

• Convert legacy SOAP text alignment output into SAM.
• Interpret mate relationships with -p when the SOAP file contains paired-end alignments.
• Preserve sequence, quality, mismatch count, and simple mate fields while moving into SAM-aware tooling.
• Bridge old SOAP-based pipelines into modern BAM-centric downstream steps.

Common Patterns

# 1) Convert single-end SOAP output
soap2sam.pl \
  alignments.soap > alignments.sam

# 2) Convert paired-end SOAP output
soap2sam.pl \
  -p \
  paired.soap > paired.sam

# 3) Convert then compress with samtools
soap2sam.pl \
  -p \
  paired.soap > paired.sam
samtools view -bS paired.sam > paired.bam

Recommended Workflow

1. Confirm the input is SOAP text output and decide whether the file is paired-end before setting -p.
2. Convert to SAM, then inspect a few records for read names, orientation flags, and mismatch tags.
3. Validate that mate pairing still makes sense if the SOAP file was reordered upstream.
4. Compress or sort with samtools only after confirming the converted SAM looks structurally correct.

Guardrails

• -p only toggles paired-end interpretation; it assumes mates arrive in the expected order and does not recover arbitrarily shuffled records.
• Help comes from Perl Getopt::Std, so --help works generically but -help is the wrong pattern for this script family.
• The script trims the quality string to sequence length if SOAP reports a longer quality field.
• Output is plain SAM records without a SAM header.