src/binarySequences.c | 2 1 + 1 - 0 !
src/readSet.c | 2 1 + 1 - 0 !
2 files changed, 2 insertions(+), 2 deletions(-)

 use the zlib distributed by debian, not the one in third-party/zlib-1.2.3/.

contrib/shuffleSequences_fasta/shuffleSequences_fasta.py | 1 1 + 0 - 0 !
1 file changed, 1 insertion(+)

 scripts need to specify interpreter in the first line

contrib/select_paired/select_paired.pl | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 s?/usr/local/perl?/usr/perl?

src/readSet.c | 2 1 + 1 - 0 !
src/readSet.h | 2 1 + 1 - 0 !
2 files changed, 2 insertions(+), 2 deletions(-)

 [patch 1/4] iscreatebinary() should not be inline

This function is used from several .c files; with inline here,
compilation with clang was broken.

Makefile | 22 11 + 11 - 0 !
1 file changed, 11 insertions(+), 11 deletions(-)

 propagate hardening options

src/correctedGraph.c | 2 1 + 1 - 0 !
src/kmerOccurenceTable.c | 2 1 + 1 - 0 !
2 files changed, 2 insertions(+), 2 deletions(-)

 fix spelling

contrib/AssemblyAssembler1.3/AssemblyAssembler1.3.py | 92 46 + 46 - 0 !
contrib/shuffleSequences_fasta/shuffleSequences_fasta.py | 4 2 + 2 - 0 !
2 files changed, 48 insertions(+), 48 deletions(-)

 use 2to3 to port to python3
Bug-Debian: https://bugs.debian.org/945743

src/readSet.c | 9 6 + 3 - 0 !
1 file changed, 6 insertions(+), 3 deletions(-)

 fix incompatible pointer types.
 Incompatible pointer types are now fatal with gcc 14 by default.
 This change fixes the following issues:
 .
 	src/readSet.c:641:21: error: assignment to gzFile {aka struct gzFile_s *} from incompatible pointer type AutoFile * [-Wincompatible-pointer-types]
 	  641 |         file.gzFile = file.autoFile = NULL;
 	      |                     ^
 	src/readSet.c: In function readFastXPair:
 	src/readSet.c:680:22: error: assignment to gzFile {aka struct gzFile_s *} from incompatible pointer type AutoFile * [-Wincompatible-pointer-types]
 	  680 |         file1.gzFile = file1.autoFile = NULL;
 	      |                      ^
 	src/readSet.c:681:22: error: assignment to gzFile {aka struct gzFile_s *} from incompatible pointer type AutoFile * [-Wincompatible-pointer-types]
 	  681 |         file2.gzFile = file2.autoFile = NULL;
 	      |                      ^