Skip to content

Fix inadvertent variable length array #2487

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

Merged
whitwham merged 1 commit into from
Dec 11, 2025
+4 −2
Merged

Fix inadvertent variable length array #2487

Changes from all commits
Commits
Show all changes
1 commit
Select commit
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
6 changes: 4 additions & 2 deletions vcfconcat.c
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -892,7 +892,8 @@ static void naive_concat(args_t *args)
int nskip;
if ( type.format==bcf )
{
const size_t magic_len = 5 + 4; // "Magic" string + header length
// Macro here as magic_len is used in an array declaration.
#define magic_len (5 + 4) // "Magic" string + header length.
uint8_t magic[magic_len];
if ( bgzf_read(fp, magic, magic_len) != magic_len ) error("\nFailed to read the BCF header in %s\n", args->fnames[i]);
// First five bytes are the "Magic" string
Expand All @@ -905,10 +906,11 @@ static void naive_concat(args_t *args)
// write only the first header
if ( i==0 )
{
if ( bgzf_write(bgzf_out, magic, magic_len) != magic_len ) error("\nFailed to write %zu bytes to %s\n", magic_len,args->output_fname);
if ( bgzf_write(bgzf_out, magic, magic_len) != magic_len ) error("\nFailed to write %d bytes to %s\n", magic_len,args->output_fname);
if ( bgzf_write(bgzf_out, tmp.s, tmp.l) != tmp.l) error("\nFailed to write %"PRId64" bytes to %s\n", (uint64_t)tmp.l,args->output_fname);
}
nskip = fp->block_offset;
#undef magic_len
}
else
{
Expand Down