Fix sam_hdr_dup to cope with long refs. #983
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The h->sdict hash is used to track references that are > 4Gb in size. The dup code didn't copy this. This manifested itself as CRAM SQ headers being truncated (read SAM hdr, dup, write as CRAM hdr). Fix by making sam_hdr_dup copy h0->sdict entries for non-parsed headers; and by making sam_hdr_update_target_arrays() update bh->sdict for parsed ones. Co-Authored-By: Rob Davies <[email protected]> Co-Authored-By: James Bonfield <[email protected]>
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This is a simplified version of the
sam_hdr_dupfix from PR #976 split out into its own pull request.If the source header has not been parsed yet (i.e.
sam_hdr_t::hrecsis NULL) it just copies any entries insam_hdr_t::sdict. If it has been parsed,sam_hdr_t::sdictentries are added insam_hdr_update_target_arrayswhere necessary.sam_hdr_update_target_arrayswill now also removesam_hdr_t::sdictentries if they are no longer needed. This fixes a bug where dangling pointers could be left insdictif any target names have been removed.Adds some
sam_hdr_duptests intest/sam.ccheck_big_ref().