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Keep a corrupt BGZF block's failure with the block so async reads don't hang - #1943
Asynchronous BGZF reading hung forever on a corrupt block; it now throws what the synchronous reader throws.
BlockCompressedInputStream.processNextBlock returns unchecked failures on the block, as it already returned IOExceptions. Before, a corrupt block's RuntimeIOException or SAMFormatException ended AsyncBlockCompressedInputStream's read-ahead task before it posted the block, so read() and then close() waited forever.
seek() rethrows a failure on the block it lands on. available() passed over a failed block like an empty one, so a seek to a truncated block succeeded and left the stream at end of file (an existing bug, and the first change would have extended it to corrupt blocks).
Tests corrupt one block of an in-memory BGZF stream (bad deflate data, negative ISIZE, CRC mismatch) and check that the async stream fails with the sync stream's exception, on a daemon thread so that a regression fails instead of hanging the suite.
…'t hang
processNextBlock returned IOExceptions on the DecompressedBlock but let
unchecked exceptions escape, and a corrupt block fails with one:
RuntimeIOException for bad deflate data or a negative ISIZE,
SAMFormatException for a bad header, a short inflate or a CRC mismatch.
On AsyncBlockCompressedInputStream's read-ahead thread that ended the
task before it posted a block or released its semaphore, so the reader
waited forever in read() and then in close().
seek() now rethrows a failure on the block it lands on. available()
passed over the failed block as it passes over an empty one, so a seek
to a truncated block succeeded and left the stream at the end of the
file, and with unchecked failures now returned on the block a seek to a
corrupt one would have done the same.
The changes capture runtime decompression failures for asynchronous BGZF reads and surface them through the reader. Seeking to truncated or corrupt blocks now reports the block error before checking availability.
Changes: BGZF error handling
Layer / File(s)
Summary
Preserve decompression failures in asynchronous reads src/main/java/htsjdk/samtools/util/BlockCompressedInputStream.java, src/test/java/htsjdk/samtools/util/AsyncBlockCompressedInputStreamTest.java
processNextBlock now captures RuntimeException as well as IOException in a DecompressedBlock. Tests compare synchronous and asynchronous failures for corrupt deflate data, negative uncompressed length, CRC mismatch, and seeking to a corrupt block.
Report errors when seeking to a block src/main/java/htsjdk/samtools/util/BlockCompressedInputStream.java, src/test/java/htsjdk/samtools/util/BlockCompressedInputStreamTest.java, CHANGELOG.md
seek checks for a decompression exception before calling available(). Tests cover seeking to truncated and corrupt blocks. The changelog records the patch-release fixes.
After a failed seek, retrying can silently report end-of-file. Fixing this narrow case is recommended before merging.
Pre-merge checks: 4 · 1
Failed checks: 1 warning
Check name
Status
Explanation
Resolution
Docstring Coverage
Docstring coverage is 66.67% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff with cyclomatic complexity of at least 2. Documenta…
Write docstrings for the functions missing them to satisfy the coverage threshold.
Passed checks: 4 passed
Check name
Status
Explanation
Description Check
Check skipped - CodeRabbit’s high-level summary is enabled.
Title check
The title clearly and concisely describes the main change: preserving corrupt BGZF block failures so asynchronous reads do not hang.
Linked Issues check
Issue #1942 requires asynchronous BGZF reads to propagate corrupt-block failures instead of hanging in read() or close(). BlockCompressedInputStream.processNextBlock now captures IOException and Runti…
Out of Scope Changes check
The production change, seek check, changelog entry, and tests all address failed BGZF block propagation or its observable behavior. The seek and truncated-block tests cover the related failure-skippin…
Full details: Linked Issues check
Explanation
Issue #1942 requires asynchronous BGZF reads to propagate corrupt-block failures instead of hanging in read() or close(). BlockCompressedInputStream.processNextBlock now captures IOException and RuntimeException in DecompressedBlock, so the read-ahead thread can post the failed block. seek() rethrows the failure before available() can skip it. The supplied test summary covers corrupt deflate data, negative ISIZE, CRC mismatch, synchronous/asynchronous exception matching, and bounded completion.
Full details: Out of Scope Changes check
Explanation
The production change, seek check, changelog entry, and tests all address failed BGZF block propagation or its observable behavior. The seek and truncated-block tests cover the related failure-skipping bug described in the current PR intent. No unrelated change is shown in the supplied whole-PR summary.
Full details: Docstring Coverage
Explanation
Docstring coverage is 66.67% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff with cyclomatic complexity of at least 2. Documentation-only edits and deletions within surviving functions are included; unchanged diff context and fully deleted functions are excluded. Analyzed 6 functions across 3 files. (1 skipped: 1 unsupported.)
Resolution
Write docstrings for the functions missing them to satisfy the coverage threshold.
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Actionable comments posted: 1
🪄 Fix comments: Fix CodeRabbit comments on this PR
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Inline comments:
Review comments at
@src/main/java/htsjdk/samtools/util/BlockCompressedInputStream.java:
- Line 408: In BlockCompressedInputStream’s seek logic, update the same-block
branch to check mCurrentBlock.mException and rethrow the stored decompression
failure, so repeating a seek to a failed block does not succeed silently.
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Asynchronous BGZF reading hung forever on a corrupt block; it now throws what the synchronous reader throws.
BlockCompressedInputStream.processNextBlockreturns unchecked failures on the block, as it already returnedIOExceptions. Before, a corrupt block'sRuntimeIOExceptionorSAMFormatExceptionendedAsyncBlockCompressedInputStream's read-ahead task before it posted the block, soread()and thenclose()waited forever.seek()rethrows a failure on the block it lands on.available()passed over a failed block like an empty one, so a seek to a truncated block succeeded and left the stream at end of file (an existing bug, and the first change would have extended it to corrupt blocks).Found while reading broadinstitute/picard#2063.
Fixes #1942
Summary by CodeRabbit