Fix issue created in PR#1848 #1849
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daviesrob
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Oct 15, 2024
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I've managed to come up with a better input to reproduce the original problem:
@SQ SN:1 LN:100
I 4 * 1 0 * * 0 0 CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
II 0 1 1 1 100M * 0 0 CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
As it makes no claim as to version or sort order, this may even be a valid SAM file.
We shouldn't be attempting to create embedded reference sequences for CRAM containers with reads mapped to chr -1 (ie unmapped). We don't permit embed_ref in multi-ref mode and it's nonsensical for entirely unmapped data. The only real fix needed here is "c->ref_id < 0" just before calling cram_generate_reference(), but checking elsewhere can sidestep other potential issues and we have safety in checking in more than one place. Credit to OSS_Fuzz Fixes oss-fuzz issue 372547397
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We shouldn't be attempting to create embedded reference sequences for CRAM containers with reads mapped to chr -1 (ie unmapped). We don't permit embed_ref in multi-ref mode and it's nonsensical for entirely unmapped data.
The only real fix needed here is
&& c->ref_id >= 0just before calling cram_generate_reference(), but checking elsewhere can sidestep other potential issues and we have safety in checking in more than one place.Credit to OSS_Fuzz
Fixes oss-fuzz issue 372547397
Note the following test triggered it, but it's only for that most recent commit and 1.21 was fine so this is a brief regression.