Skip to content

Force standard 28 bytes empty BGZF GZIP block for no compression BAM #7

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
peterjc wants to merge 4 commits into
base: master
Choose a base branch
from
Open

Force standard 28 bytes empty BGZF GZIP block for no compression BAM #7

Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
f7d8969
Force standard 28 bytes empty BGZF GZIP block for no compression BAM …
peterjc Nov 17, 2011
dee0acf
Tweak patch following comments from John Marshall
peterjc Nov 17, 2011
b997645
Fix compression level, not zero for a 28 byte EOF block
peterjc Nov 17, 2011
17314c0
Use Z_DEFAULT_COMPRESSION constant, thanks John
peterjc Nov 17, 2011
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 3 additions & 0 deletions bgzf.c
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -627,6 +627,9 @@ int bgzf_close(BGZF* fp)
if (fp->open_mode == 'w') {
if (bgzf_flush(fp) != 0) return -1;
{ // add an empty block
// add 28 bytes EOF empty block
fp->compress_level=Z_DEFAULT_COMPRESSION; //don't need value again
// (different compression levels would give different empty blocks)
int count, block_length = deflate_block(fp, 0);
#ifdef _USE_KNETFILE
count = fwrite(fp->compressed_block, 1, block_length, fp->x.fpw);
Expand Down