Detect swapped arguments, harden error reporting, and add NO_COLOR support

[mmokrejs]

Summary

This PR improves miniprot's error handling for pipeline callers that rely on exit codes and stderr messages.

Commit 1: Detect DNA queries and exit with non-zero code

When the query file contains DNA instead of protein sequences (>80% A/C/G/T/N residues), miniprot now emits a clear error message and returns exit code 1. Previously, swapping the <ref.fa> and <query.faa> arguments would cause miniprot to silently run to completion with exit code 0, producing no useful output.

Commit 2: Harden argument validation, error reporting, and NO_COLOR support

• Unrecognized options → exit 1: Previously continued silently with exit 0, which is dangerous for pipeline callers where a typo in a flag silently runs with wrong parameters.
• Missing arguments → specific error: Instead of just dumping the usage text, miniprot now prints [ERROR] missing query protein file or [ERROR] missing arguments before the usage.
• File errors → include filename: Index load and mapping failure messages now include the filename.
• Deprecated -s → hard error: Was silently ignored; now exits with a clear deprecation message.
• Validate all atoi()/atof() calls: Passing invalid values like --outs=abc now produces [ERROR] invalid numeric value 'abc' for --outs instead of silently setting the value to 0.
• NO_COLOR support (no-color.org): All hardcoded \033[1;31m ANSI escapes across main.c, map.c, bseq.c, and options.c are replaced with MP_COLOR_RED/MP_COLOR_RESET macros that respect the NO_COLOR environment variable and isatty(stderr).

Motivation

When miniprot is called from a bioinformatics pipeline (e.g., via subprocess.run(..., check=True) in Python), the caller relies on the exit code to detect failures. The current behavior of returning exit 0 on swapped arguments, unrecognized options, or invalid numeric values makes it impossible to reliably detect misconfigurations.

Testing

Verified with 9 functional tests covering all error paths and normal operation.

[codacy-production]

Up to standards ✅

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🟢 Metrics 27 complexity · 0 duplication

Metric	Results
Complexity	27
Duplication	0

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