Cap hts_getline() return value at INT_MAX #1448
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On success, hts_getline() returns the length of the string read. Its return type is int, so when plain int is 32 bits, trouble ensues for very long lines exceeding 2GiB: the return value wraps to negative and is misinterpreted as error. Rather than changing the return type to e.g. ssize_t, clamp the return value for very long lines. In test/sam.c's test cases, check the return value is indeed the expected length.
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Something I noticed while writing a script to generate an enormous VCF record for #1447: the initial version of this generated a 2.5 GiB VCF record line, but
vcf_read()failed to read it.It turns out that
kgetline2()(as used byhts_getline()for uncompressed input) reads such a line without trouble, buthts_getline()truncates the read string's length tointand returns negative — thus indicating error rather than a successfully read line.This PR clamps the successful return value at
INT_MAX. An alternative would be to change the return type to e.g.ssize_t, but this would have potential ABI implications perhaps…In practice, no
hts_getline()invocations in htslib, samtools, or bcftools use the length returned at all; they only use the return value to distinguish between success/EOF/error. Other third-party code potentially may use the length.Also add to the existing basic
hts_getline()tests In test/sam.c: check that the successful return value is indeed the expected length.