Ace2sam

# 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.