Fix big-endian test failures and use-after-free issues in error handling #2408
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On little-endian hosts, `int` here caused incorrect results at positions beyond the range of int. On big-endian hosts, it caused incorrect results at all positions.
Calling bgzf_close() (and hts_close()) frees the file pointer, so the errcode field cannot be accessed afterwards. Report errors as per errno instead as is done in vcfconvert.c. Also report the right file pointer's errcode after bgzf_write() failure.
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The incorrect type in
mpileup_get_val()in plugins/vrfs.c caused incorrect results and test failures on big-endian machines, asposwas essentially always set to 0 (being the high-order bits of theint64_t).Accessing
fileptr->errcodeafter closing thefileptris invalid as generally the file structure will have been deallocated. This replaces that withstrerror(errno), as is already done in vcfconvert.c. Also report the right file pointer'serrcodeafterbgzf_write()failure.And some other Makefile fixes and other miscellanea.