Fix sam_hdr_dup to cope with long refs.#983
Merged
jkbonfield merged 1 commit intosamtools:developfrom Nov 20, 2019
Merged
Conversation
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]>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
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().