Reheader external

[valeriuo]

Allow an external application to modify the header of the target file and pass back the result to samtools. The external app will read the original header through stdin and output the modified header on stdout.

Fixes #999.

[jmarshall]

If you open the file with hopen() followed by hts_hopen(), you will already have the hFILE* and won't have a desire for an hts_hfile() function.

[jmarshall]

1. The conventional option letter for stuff like this is -c / --command. cf bash, su.

2. If you organised this via a function like

bam_hdr_t *rewrite_header(bam_hdr_t *input_header) {
    if (g_external_command_mode) return do_popen(g_command, input_header);
    else return do_sam_hdr_read(g_header_filename);
}

that was called from inside each of the bam/cram_reheader functions, you wouldn't have any need to rewind the input.

3. It looks like the external program is always given the header in SAM format. IMHO that's the right thing to do, but it should be documented.

[valeriuo]

Thanks for the review and suggestions.