Write CG as B:I, encode SAM/BAM/CRAM text as the spec describes, and refuse text that would corrupt it - #1840
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A CIGAR with more than 65535 operators does not fit in a BAM record, so BAMRecordCodec writes a placeholder CIGAR and puts the real one in a CG tag. It wrote the tag as B:i; the SAM specification says B:I, and older samtools releases reject B:i (issue #1560).
SAM text has no escapes, so a tab or line break inside a value ends its field or its line, and the rest of the value is read back as further fields or lines: a read group whose description was "x<TAB>PI:123" came back with a PI tag (issue #1108). Such values are now rejected with an IllegalArgumentException that shows the value. - Header: every tag value, including @rg and @pg IDs, is checked in TextTagCodec.encodeUntypedTag, and a comment may not contain a line break (tabs in @co stay allowed). BAM and CRAM headers are SAM text, so this covers all three formats. @sq SN was already restricted to the spec's name characters. - Records: SAMTextWriter.writeAlignment checks the read name and every Z and A tag before it writes anything, so a rejected record leaves no partial line. SAMRecord.toString(), which uses the same formatting, does not check and does not throw. Writing SAM text is about 4.5% slower on a WGS BAM whose reads carry OQ (about 240 characters of Z values per record); the scan uses a single comparison per character in the common case.
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Included review availability: Your plan provides up to 2 included reviews per hour; 0 remain after this review. 📝 WalkthroughWalkthroughThe change adds destination-specific validation for text written to SAM, BAM, and CRAM. It also sets explicit encodings for headers, read names, and tags, including ISO-8859-1 handling for one-byte values and UTF-8 header decoding with an ISO-8859-1 fallback. ChangesText encoding and validation across SAM, BAM, and CRAM
Priority: ➖ Normal Estimated code review effort: 4 (Complex) | ~45 minutes Change: Bug fix Merge Risk: 🟡 Moderate · up to A long-CIGAR BAM record with invalid text can still bypass validation and be re-encoded as malformed data. Close this narrow data-integrity gap before merging. Security Architecture ReviewSecurity architecture risk: 🟡 Moderate · up to The new checks reduce the chance of writing corrupt files, but changes across three widely used formats warrant compatibility and failure-recovery review. No newly worsened security attack path was established. Retained concerns Security review detailsSecurity Blast Radius
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Inline comments:
In `@CHANGELOG.md`:
- Line 251: Update the first sentence of the changelog entry to distinguish
header values from header comments, so it does not imply that tabs in `@CO`
comments cause an exception; retain the stated allowance for tabs in `@CO`
comments.
In `@src/main/java/htsjdk/samtools/TextTagCodec.java`:
- Line 152: Update the delimiter validation in TextTagCodec to reject characters
whose byte-cast output is tab, LF, or CR, while preserving the rule that permits
literal tabs where required. In SAMTextHeaderCodec, reject comment characters
whose emitted bytes become LF or CR, but continue permitting tabs. Apply these
changes at both affected sites.
- Line 141: Validate tagName in TextTagCodec before serialization, rejecting
names that are not valid two-character SAM tag names; only append the validated
name and value so untrusted keys cannot inject additional header fields.
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CHANGELOG.mdsrc/main/java/htsjdk/samtools/BAMRecordCodec.javasrc/main/java/htsjdk/samtools/SAMTextHeaderCodec.javasrc/main/java/htsjdk/samtools/SAMTextWriter.javasrc/main/java/htsjdk/samtools/TextTagCodec.javasrc/test/java/htsjdk/samtools/BAMRecordCodecTest.javasrc/test/java/htsjdk/samtools/SAMTextHeaderCodecTest.javasrc/test/java/htsjdk/samtools/SAMTextWriterTest.javasrc/test/java/htsjdk/samtools/TextTagCodecTest.java
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…s that would corrupt it htsjdk encoded text differently in every format: SAM headers were read as UTF-8 and BAM headers as ISO-8859-1, both were written one byte per char (so a char above 0xFF lost its high byte, and U+010D became a carriage return), CRAM headers used the platform charset, CRAM read names were UTF-8 and CRAM Z tags ASCII. The SAM spec says a SAM file is UTF-8 with non-ASCII allowed only in @co and DS and CL values, and htslib passes every other field through byte for byte (issue #1202). - Header text is UTF-8 in all three formats. A header line that is not valid UTF-8, as htsjdk 5.x wrote non-ASCII ones, is read as ISO-8859-1; BAM and CRAM headers now go through SamLineReader to get the same per-line fallback. AsciiWriter gains writeUtf8 for the SAM header. - Read names and Z and A tags stay one byte per char and are read and written as ISO-8859-1 everywhere, so bytes 0x80-0xFF that other tools wrote pass through unchanged. That fixes the CRAM 3.1 name tokeniser, which round-tripped such bytes through UTF-8 and ASCII and returned '?', CRAM Z tags, and the BAM and CRAM A-tag decoders, which sign-extended a byte above 0x7F to a char near 0xFFFF. - WritableText holds the rules for what each destination cannot hold: a tab, line break or NUL in a header tag name or value; a line break or NUL in @co; those or a char above 0xFF in a SAM record's read name or Z/A tags; and a NUL or char above 0xFF in BAM and CRAM, whose strings are NUL-terminated. BAMRecordCodec checks only records it re-encodes, so a record read from BAM and written back unchanged is copied as it was read. CRAMContainerStreamWriter checks every record. - Header tag names get the same check as values, from review.
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- 🪄 Fix CodeRabbit comments on this PR
🤖 Prompt to fix review comments
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Inline comments:
In `@src/main/java/htsjdk/samtools/BAMRecordCodec.java`:
- Around line 107-109: Move WritableText.requireInRecord from the initial cache
check into the re-encoding branch of BAMRecordCodec, after the final
variableLengthBinaryBlock check and immediately before encoding the
variable-length fields. This ensures validation runs when a stale cache forces
re-encoding while leaving the unchanged cached-block write path untouched.
In `@src/main/java/htsjdk/samtools/util/AsciiWriter.java`:
- Line 85: Update AsciiWriter.writeUtf8 to reject unpaired UTF-16 surrogates
before encoding, using surrogate-pair validation or a UTF-8 encoder configured
to report malformed input. Preserve valid UTF-8 output while preventing
String.getBytes from silently replacing malformed input.
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CHANGELOG.mdsrc/main/java/htsjdk/samtools/BAMFileReader.javasrc/main/java/htsjdk/samtools/BAMFileWriter.javasrc/main/java/htsjdk/samtools/BAMRecordCodec.javasrc/main/java/htsjdk/samtools/BinaryTagCodec.javasrc/main/java/htsjdk/samtools/CRAMContainerStreamWriter.javasrc/main/java/htsjdk/samtools/SAMTextHeaderCodec.javasrc/main/java/htsjdk/samtools/SAMTextWriter.javasrc/main/java/htsjdk/samtools/TextTagCodec.javasrc/main/java/htsjdk/samtools/WritableText.javasrc/main/java/htsjdk/samtools/cram/build/CramIO.javasrc/main/java/htsjdk/samtools/cram/compression/nametokenisation/NameTokenisationDecode.javasrc/main/java/htsjdk/samtools/cram/compression/nametokenisation/NameTokenisationEncode.javasrc/main/java/htsjdk/samtools/cram/encoding/reader/CramRecordReader.javasrc/main/java/htsjdk/samtools/cram/encoding/writer/CramRecordWriter.javasrc/main/java/htsjdk/samtools/cram/structure/Container.javasrc/main/java/htsjdk/samtools/cram/structure/ReadTag.javasrc/main/java/htsjdk/samtools/util/AsciiWriter.javasrc/main/java/htsjdk/samtools/util/SamLineReader.javasrc/test/java/htsjdk/samtools/BAMFileReaderTest.javasrc/test/java/htsjdk/samtools/BAMFileWriterTest.javasrc/test/java/htsjdk/samtools/BAMRecordCodecTest.javasrc/test/java/htsjdk/samtools/BinaryTagCodecTest.javasrc/test/java/htsjdk/samtools/CRAMContainerStreamWriterTest.javasrc/test/java/htsjdk/samtools/SAMTextHeaderCodecTest.javasrc/test/java/htsjdk/samtools/SAMTextWriterTest.javasrc/test/java/htsjdk/samtools/TextTagCodecTest.javasrc/test/java/htsjdk/samtools/cram/build/CramIOTest.javasrc/test/java/htsjdk/samtools/cram/compression/nametokenisation/NameTokenisationTest.javasrc/test/java/htsjdk/samtools/cram/encoding/CramRecordWriterReaderTest.javasrc/test/java/htsjdk/samtools/cram/structure/ContainerTest.javasrc/test/java/htsjdk/samtools/cram/structure/ReadTagTest.javasrc/test/java/htsjdk/samtools/util/AsciiWriterTest.javasrc/test/java/htsjdk/samtools/util/SamLineReaderTest.java
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- src/test/java/htsjdk/samtools/TextTagCodecTest.java
- src/test/java/htsjdk/samtools/SAMTextHeaderCodecTest.java
- src/main/java/htsjdk/samtools/SAMTextHeaderCodec.java
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…unpaired surrogates in headers getCigar() moves a long CIGAR out of a CG tag and marks the record changed, so the check of a record BAMRecordCodec re-encodes now runs after it, still before anything is written or the CG tag is set. UTF-8 cannot encode half a surrogate pair, and String.getBytes writes a question mark for one, so a header value or comment holding one is refused; whole pairs are written as before.
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Write a long CIGAR's CG tag as
B:I, encode SAM/BAM/CRAM text as the spec describes, and refuse values that would corrupt the file.BAMRecordCodecstores a CIGAR with more than 65535 operators inCG:B:I, as the spec says; it wroteB:i, which older samtools releases reject.@CO,DSandCL). Read as UTF-8, falling back to ISO-8859-1 per line for headers older htsjdk wrote. SAM/BAM headers used to be written one byte per char (čbecame a CR) and BAM headers read as Latin-1.?, and BAM/CRAM A tags sign-extending them.IllegalArgumentExceptionfor what would corrupt the output (all checks are in the newWritableText):@CO: line break, NUL;BAMRecordCodec.encodealone, every record re-encoded, +13.3%; a whole BAM write at default compression +1.8% (all t ≈ 5). The cost is the character scan itself; performance work is planned after the functional changes land.Supersedes #1569.
Summary by CodeRabbit
Compatibility
0x7F.Validation
U+00FFwhere only single-byte text is supported.Bug Fixes
CGtag.