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Preserve bounded BAM stream errors without pipe seek failures - #111
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A Sid ONT partner-query timeout interrupted a buffered BAM header. Pysam then raised an unraisable
Illegal seekerror while destroying its partially constructed AlignmentFile on the pipe. An offline producer that flushes a partial BGZF header and stalls reproduces the same cleanup failure.Read the forward-only BAM framing through Python's gzip reader and copy original header/record blocks to a local BGZF file. This avoids constructing AlignmentFile on a pipe and preserves stored SEQ, QUAL, CIGAR, tag widths and float payloads. Keep the process deadline, overflow cap, stderr, and kill/reap cleanup; truncated streams and nonzero producers still fail without publishing a partial derivative. Version: 0.15.4.
Validation: ruff and all 412 tests passed. New regressions exercise large headers, mid-header timeouts with no unraisable cleanup error, exact record multiplicities after success, overflow, truncated compressed/record blocks, nonzero exit with stderr, and successful acquisition after failure. This fixes the secondary cleanup exception; it does not claim to fix slow remote queries.
Fixes #106. Related: openvax/isovar#436.