ace2sam

name	ace2sam
description	Use when converting ACE assembly files into SAM while preserving legacy ACE-specific padded or contig-sequence behavior.
disable-model-invocation	true
user-invocable	true

ace2sam

Quick Start

• Command: ace2sam [-p] [-c] assembly.ace > alignments.sam 2> header.txt
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/ace2sam
• Reference: See references/help.md

When To Use This Tool

• Convert legacy ACE assembly files into SAM for downstream inspection with SAM/BAM-aware tools.
• Preserve ACE padding with -p when you need padded coordinate representation.
• Emit contig sequence information with -c when reconstructing richer reference context from ACE.
• Bridge older assembly/editing workflows into modern SAM-centric tooling.

Common Patterns

# 1) Convert ACE to SAM, capturing stderr header text separately
ace2sam \
  assembly.ace > assembly.sam 2> assembly.header.txt

# 2) Keep padded coordinates in the SAM body
ace2sam \
  -p \
  assembly.ace > assembly.padded.sam 2> assembly.header.txt

# 3) Include contig sequence information
ace2sam \
  -c \
  assembly.ace > assembly.with-contigs.sam 2> assembly.header.txt

Recommended Workflow

1. Validate that the input really is ACE and still follows the ordering assumptions expected by the converter.
2. Decide whether downstream consumers need padded coordinates (-p) or contig sequence output (-c) before conversion.
3. Capture stdout and stderr separately so you do not lose the header text emitted on stderr.
4. Inspect a few output records before loading the converted SAM into later tools.

Guardrails

• ace2sam does not use GNU-style long flags; --help and --version are treated as invalid short-option bundles before usage text is shown.
• The program writes header text to stderr and the headerless SAM body to stdout; redirect both deliberately.
• Input ACE fields must appear in the documented order (CO->[BQ]->(AF)->(RD->QA)), and the read order in AF and RD must match.
• -p changes coordinate semantics by emitting padded SAM, so do not mix padded and unpadded outputs in the same downstream workflow.