Fix broken pipe error when piping to early-exit commands

[Copilot]

The CI tests fail with "Unable to flush stdout: Broken pipe" when piping any2fasta to commands like grep -m 1 that exit after finding their first match.

Changes

• Ignore SIGPIPE signals to prevent immediate termination when the pipe reader closes
• Handle EPIPE errno gracefully in explicit STDOUT close, exiting cleanly instead of failing
• Use POSIX::EPIPE constant instead of hardcoded errno value

use POSIX qw(EPIPE);

$SIG{PIPE} = 'IGNORE';

# ... script body ...

close(STDOUT) or do {
  exit(0) if $! == EPIPE;
  die "Error closing stdout: $!\n";
};

This allows commands like any2fasta test.gbk | grep -m 1 pattern to exit cleanly without errors.

Original prompt

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This section details on the original issue you should resolve

<issue_title>CI: Unable to flush stdout: Broken pipe</issue_title>
<issue_description>I am getting this error in my tests in CI.yml Actions:

Unable to flush stdout: Broken pipe
Error: Process completed with exit code 1.

</issue_description>

Comments on the Issue (you are @copilot in this section)

• Fixes CI: Unable to flush stdout: Broken pipe #31

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