cram: Clarify the preservation map's reference required flag for unmapped slices

[zaeleus]

This is in regard to CRAM format specification (version 3.1) (2024-09-04).

§ 8.4.1 "Compression header block: Preservation map" describes the reference required (RR) flag as "true if reference sequence is required to restore the data completely". If this is true and the records do not require a reference sequence to restore the data (e.g., an unmapped slice), is it considered an invalid state?

As I understand it, this flag should be false if the slice is unmapped, but some implementation don't set it as such, e.g., htslib:

$ samtools --version | head -2
samtools 1.21
Using htslib 1.21

$ (
samtools view --output-fmt cram <<EOF
@HD	VN:1.6
r1	4	*	0	0	*	*	0	0	NNNN	!!!!
EOF
) | cram_dump - | grep --after-context 4 "Preservation map" | head -5
      Preservation map:
        SM => 30398990 (0x1cfda0e)
        TD => 30398986 (0x1cfda0a)
        RN => 1 (0x1)
        AP => 1 (0x1)

All the records in this slice are unmapped (cram_dump: "Slice ref seq -1"), and this implicitly sets the reference required field to true, as per "The boolean values are optional, defaulting to true when absent..." However, a reference sequence is not required to decode this.