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fix(bam-io): point empty stdin/pipe input at the upstream stage - #866
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Included review availability: 0 reviews are currently available. Your included PR review attempts over the past 7 days set your current allowance at 1 review per hour. WalkthroughEmpty SAM diagnostics now distinguish regular files, stdin-like paths, FIFOs, descriptor paths, and empty gzip members. Parameterized tests cover source detection and diagnostic wording. ChangesEmpty-input diagnostics
Estimated code review effort: 2 (Simple) | ~10 minutes Merge Risk: ⚪ Minimal · up to This change improves empty-stream diagnostics by directing stdin and pipe failures toward the upstream producer while preserving regular-file behavior. No actionable merge-blocking risk remains after normal checks and review. 🚥 Pre-merge checks | ✅ 3✅ Passed checks (3 passed)
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Additional details and impacted files@@ Coverage Diff @@
## main #866 +/- ##
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- Coverage 94.68% 94.54% -0.14%
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Files 193 268 +75
Lines 119865 141788 +21923
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+ Hits 113490 134051 +20561
- Misses 6375 7737 +1362 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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Inline comments:
In `@crates/fgumi-bam-io/src/sam_input.rs`:
- Line 426: Update the Rust documentation comment near the SAM input handling
code to format the stat identifier as inline code using backticks, without
changing the surrounding wording.
- Around line 432-440: Update the descriptor-path classification logic to
attempt metadata lookup before accepting the /dev/fd/ or /proc/self/fd/
prefixes: return pipe-like only when the resolved file type is_fifo(), and
retain the prefix check solely when metadata lookup fails.
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crates/fgumi-bam-io/src/sam_input.rs
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Inline comments:
In `@crates/fgumi-bam-io/src/sam_input.rs`:
- Line 651: Add Unix-only diagnostic tests around the existing input-path table
in sam_input.rs to cover both the is_fifo() metadata branch and the
/proc/self/fd/N fallback, while preserving the current stdin and /dev/fd/N
cases.
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crates/fgumi-bam-io/src/sam_input.rs
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When a command reads from stdin or a `-` pipe and the stream closes with no records, the reader reported "Input is empty", which reads as a user error about an empty file. In a pipe the usual cause is an upstream stage exiting before writing — a crash, an OOM kill, a pipefail abort — so the empty-file wording sends debugging in the wrong direction. Distinguish the source via the existing is_stdin_path: for a regular file keep the "Input is empty" wording; for stdin/`-` say the stream closed before any records arrived and point at the feeding command's exit status and logs. Applies to both the direct and gzip-member empty cases.
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When a command reads from stdin or a
-pipe and the stream closes with no records,normalize_to_bgzfreportedInput is empty: <path> (expected BAM or SAM records). That reads as a user error about a genuinely empty file.In a pipe, an empty input almost always means an upstream stage exited before writing anything — a crash, an OOM kill, a
set -o pipefailabort. The "empty input" wording then sends debugging in the wrong direction: at the reader that hit EOF, not at the producer that died.Change
Route both
InputFormat::Emptysites (direct and gzip-member) through a newempty_input_error(path, file_desc)helper that keys on the existingis_stdin_path:Input is empty: <path> (expected BAM or SAM records)-→No records read from <path> (expected BAM or SAM records): the input stream closed before any records arrived. In a pipe this usually means an upstream stage exited or was killed (for example, out-of-memory) before writing — check the exit status and logs of the command feeding this one.Tests
Two unit tests in
sam_input: an empty regular-file path keeps the "Input is empty" wording;-and/dev/stdinget the upstream-pointing message and never say "Input is empty".cargo test -p fgumi-bam-io(168 passed); clippy and fmt clean.Notes / possible follow-ups
is_stdin_path:-,/dev/stdin), covering the common pipe case. A named FIFO passed by path would still get the file wording; afstat-basedis_fifo()check could extend it if wanted.Broken pipe (os error 32)on the producer) is untouched here; a clearer "downstream stage closed the pipe" message could be a separate change.Risk: command output changes: diagnostics only; grouping, consensus, sort order, corrected UMIs, and metrics are unchanged;
unsafechanges: none, so theCLAUDE.mdallowlist is unchanged; memory bounds, queue capacity, and thread/backpressure policy changes: none.Fixes source-aware empty-input diagnostics in
normalize_to_bgzf. Regular files retainInput is empty. Pipe-like inputs report that the stream closed before records arrived and direct users to upstream status and logs. Empty gzip members use the same routing. Tests cover regular files,-,/dev/stdin, pipe-like paths, and gzip members.