maq2sam-short

name	maq2sam-short
description	Use when converting legacy MAQ short-map files into SAM for downstream SAMtools-compatible processing.
disable-model-invocation	true
user-invocable	true

maq2sam-short

Quick Start

• Command: maq2sam-short reads.map [readGroup] > reads.sam
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/maq2sam-short
• Reference: See references/help.md

When To Use This Tool

• Convert legacy MAQ .map alignment output into SAM.
• Preserve an older MAQ-based alignment result while moving it into current SAM/BAM tooling.
• Attach a simple trailing read-group label when you need to distinguish converted cohorts.
• Use this specific binary for the MAQ short-map flavor rather than the long-map variant.

Common Patterns

# 1) Convert a MAQ short-map file to SAM
maq2sam-short \
  reads.map > reads.sam

# 2) Add a read-group label during conversion
maq2sam-short \
  reads.map RG1 > reads.rg.sam

# 3) Convert then hand off to samtools
maq2sam-short \
  reads.map > reads.sam
samtools view -bS reads.sam > reads.bam

Recommended Workflow

1. Confirm the input really is the MAQ short-map flavor before choosing this binary.
2. Decide whether you want to attach the optional trailing read-group label during conversion.
3. Convert to SAM, then inspect a few records before turning the file into BAM or mixing it with other alignments.
4. Keep the original .map file because these legacy converters expose almost no self-describing metadata.

Guardrails

• maq2sam-short does not implement real --help or --version; those strings are treated like filenames and trigger usage text only after a file-open failure.
• The optional second positional argument is just a trailing read-group label, not a full SAM @RG header definition.
• Use the short-map converter only for the matching MAQ map flavor; the usage text does not autodetect the correct variant for you.
• Output is plain SAM records and should be inspected before downstream compression or merging.