fix for incorrect failure message with invalid reference file and crash fix

[vasudeva8]

This change is for #1723 where misleading failure message is displayed.
The error number is reset if it is due to reference file access before reporting the error, to avoid misleading message.
Another change is made to avoid crash/invalid access in hts_close.
A change in samtools will also be raised to do null check before invoking hts_close.

[daviesrob]

Rather than reset errno unconditionally, it would be better to take a copy before calling hts_opt_apply() and then use that to restore the old value if necessary. It might also be good to only do this if errrno is ENOENT, so we only suppress the "No such file or directory" errors and leave others alone.

E.g. something like this:

    if (fmt && fmt->specific) {
        int save_errno = errno;
        if (hts_opt_apply(fp, fmt->specific) != 0) {
            if (((hts_opt*)fmt->specific)->opt == CRAM_OPT_REFERENCE  && errno == ENOENT) {
                //reset error on reference file to avoid incorrect error report
                errno = save_errno;

[vasudeva8]

made changes as discussed.

[daviesrob]

Having tested this, it looks like refs_load_fai already reports this error, so we probably don't need to do it again here after all. Although making refs_load_fai print the error message might be useful:

samtools stats --reference /foo 9305_4#1c.cram
[E::fai_build3_core] Failed to open the file /foo
[E::refs_load_fai] Failed to open reference file '/foo'
[E::hts_open_format] Couldn't load reference "/foo" : No such file or directory
[E::hts_open_format] Failed to open file "9305_4#1c.cram"
samtools stats: failed to open "9305_4#1c.cram"