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Use when converting ACE assembly files into SAM while preserving legacy ACE-specific padded or contig-sequence behavior.
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Based on SOC occupation classification
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| 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 [-p] [-c] assembly.ace > alignments.sam 2> header.txt/home/vimalinx/miniforge3/envs/bio/bin/ace2sam-p when you need padded coordinate representation.-c when reconstructing richer reference context from ACE.# 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
-p) or contig sequence output (-c) before conversion.ace2sam does not use GNU-style long flags; --help and --version are treated as invalid short-option bundles before usage text is shown.stderr and the headerless SAM body to stdout; redirect both deliberately.(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.