Fix segfault due to ";HRUN=3" INFO field #95
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jmarshall
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Thanks for reporting John! I think I found the culprit for the truncated info field (I used the same char* twice in sprintf, which leads to undefined results according to the POSIX standard; sorry this was shoddily written). Just committed a fix with 8206db2 (more exactly 1e44677). Your changes make certainly sense in addition. Will merge as soon as it's confirmed that this was indeed the culprit. Many thanks again |
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Yep, your fix looks okay and stops the malformed I don't think there was anything undefined about the sprintfs; it was just a bug in that it overwrote the text that you had already put in |
Previously any key would be returned as being matched by the empty "key=value" at the start of ";HRUN=3" (which is invalid VCF). This resulted in a crash when e.g. lofreq_filter.c looking for "SB" expected a value but in this case the returned sb_char was NULL. Crash fixed by no longer returning a hit for "SB" in this case. (Also convert a couple of previously missed legacy samtools API usages.)
jmarshall
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…pushed a more complete fix for the don't recognise |
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Thanks again @jmarshall and @bgruening ! |
Fix
vcf_var_has_info_key()'s key comparison, which causes the crash in #89 due to;HRUN=3:Previously any key would be returned as being matched by the entirely empty "key=value" at the start of ";HRUN=3". Note that INFO is semicolon-separated, so this is in fact invalid VCF.
This resulted in a crash when e.g. lofreq_filter.c looking for "SB" expected a value but in this case the returned sb_char was NULL. Crash fixed by no longer returning a hit for "SB" in this case.
(Also convert a couple of previously missed legacy samtools API usages. Oops.)