As the … in the ##contig=<ID=…> lines unambiguously denotes a contig name (and there are no region strings anywhere near ID in the grammar, such as it is), passing this to _regions_init_string() as is is clearly a bcftools (or htslib) bug. Whatever the code is trying to do, it needs to do it by calling a dumber function that accepts only a contig name […]
The dumber function already exists and is already used by this code for all but the first contig header line. The code used _regions_init_string() rather than _regions_add() only when needed the first time to allocate a new bcf_sr_regions_t structure; instead extract basic initialisation into a new bcf_sr_regions_alloc() function and use _regions_add() exclusively.
As a bonus, the new function actually checks that the memory allocation succeeded. Use the new function throughout.
jkbonfield
commented
1 month ago
Quoting from samtools/bcftools#2179:
The dumber function already exists and is already used by this code for all but the first contig header line. The code used
_regions_init_string()rather than_regions_add()only when needed the first time to allocate a newbcf_sr_regions_tstructure; instead extract basic initialisation into a newbcf_sr_regions_alloc()function and use_regions_add()exclusively.As a bonus, the new function actually checks that the memory allocation succeeded. Use the new function throughout.
Fixes samtools/bcftools#2179.