Add optional progress output for long-running subcommands (mpileup, view, norm, index)

[carstenerickson]

Summary

bcftools mpileup, view, norm, and index run silent on multi-hour inputs, making "still working" indistinguishable from "hung" without external tooling. An opt-in periodic stderr progress line would close the gap at near-zero cost.

Current workaround

We read /proc/<pid>/io (Linux only) for bytes-read and divide by input file size. Limitations:

• Linux only; no /proc/<pid>/io on macOS or BSD.
• Bytes only, no record counts.
• Fragile child-PID discovery when bcftools sits behind a shell pipe.
• mpileup needs a special case because the I/O-doing process is the child, not the parent shell.

Our wrapper is ~140 LOC handling these edges.

Suggested approach

Either of:

• Opt-in flag — --progress[=INTERVAL] emits a stderr line every INTERVAL records (default 1M). One extra branch per record; off by default, so scripts are unaffected.
• TTY auto-enable — isatty(STDERR_FILENO)-gated, like tar --checkpoint=.N. Interactive only, no flag.

Format suggestion:

[mpileup] 12.3 / 23.0 GB processed (53.5%), 145M records, 1234s elapsed, 11min remaining

Bytes from htsFile.fp.bgzf->block_offset; records from each subcommand's main loop; ETA from linear extrapolation, omitted when input size is unknown.

Low priority — the workaround works. Filing because the proliferation of /proc/<pid>/io wrappers across pipelines is a UX signal that upstream should own this.

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bcftools 1.23.1.