Allow bcftools reheader --fai to read its input file from a stream #2129
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−45
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This didn't work in the past because update_from_fai() opened, read the header from, and then closed the input file, preventing the reheader_* functions from accessing the rest of the file contents when the input is a stream. As all the reheader_* functions read the header into a kstring, it's possible to make streaming work by passing this kstring into update_from_fai() and adjusting it to work directly on that copy of the data. As update_from_fai() no longer needs to write a temporary file, args_t::rm_tmpfile and args_t::tmp_prefix can be removed. The -T option is ignored as it's no longer needed, but is still accepted for compatibility. The init_tmp_prefix() function is still used by some other bcftools subcommands, so is left in place for now.
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Thank you @daviesrob 🙏 ! |
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This didn't work in the past because update_from_fai() opened, read the header from, and then closed the input file, preventing the reheader_* functions from accessing the rest of the file contents when the input is a stream. As all the reheader_* functions read the header into a kstring, it's possible to make streaming work by passing this kstring into update_from_fai() and adjusting it to work directly on that copy of the data.
As update_from_fai() no longer needs to write a temporary file, args_t::rm_tmpfile and args_t::tmp_prefix can be removed. The -T option is ignored as it's no longer needed, but is still accepted for compatibility. The init_tmp_prefix() function is still used by some other bcftools subcommands, so is left in place for now.
Fixes #2088