Use only _regions_add() in synced_bcf_reader.c when adding the list of contig names #1781
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Don't use _regions_init_string(), which misinterprets contig names containing colons as region specification strings. The code used _regions_init_string() rather than _regions_add() only when needed to allocate a new bcf_sr_regions_t structure; instead extract basic initialisation into a new bcf_sr_regions_alloc() function, which as a bonus checks the memory allocation. Use the new function throughout. Fixes samtools/bcftools#2179.
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Thanks John |
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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.