Check fclose(stdout) at the end of main() [and miscellanea] #2046
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Since PR samtools/htslib#1665, hts_open("-", "w") / hts_close() no longer actually closes stdout. Close it at the end of main() so there is an opportunity to detect I/O errors in previously-uncommitted writes. Ignore EBADF as other code may have already closed stdout, e.g., either particular subcommands or when (dynamically) linked against an older version of HTSlib.
Other source files that use strcase*() functions #include <strings.h> themselves, so do so for this source file too. (<strings.h> is often a byproduct of <string.h> but POSIX doesn't require that.)
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Similar to samtools/samtools#1909, this is a companion pull request to samtools/htslib#1665. Now that
hts_open("-", "w")/hts_close()no longer actually closes stdout. Close it explicitly at the end ofmain()when a subcommand may have written to stdout, so there is an opportunity to detect I/O errors in previously-uncommitted writes.Ignore EBADF as other code may have already closed stdout, e.g., either particular subcommands or when (dynamically) linked against an older version of HTSlib.
Also trivially: include
<strings.h>where needed to ensurestrcasecmp()et al are declared. (<strings.h>is often a byproduct of<string.h>but POSIX doesn't require that.)