scripts/stacks-hist2d-loci-samples-coverage | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 alter script interpreter

Makefile.am | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

 fix script exe_paths
 denovo_map.pl and other stacks scripts hard-code the binary paths to the
 installation directory. However, we move these binaries to /usr/lib/stacks/bin,
 which breaks these scripts. This hard-codes the binary path to the correct
 location.

Makefile.am | 4 2 + 2 - 0 !
configure.ac | 4 2 + 2 - 0 !
2 files changed, 4 insertions(+), 4 deletions(-)

 use debian packaged version of htslib

src/clone_filter.cc | 2 1 + 1 - 0 !
src/gstacks.cc | 4 2 + 2 - 0 !
src/kmer_filter.cc | 8 4 + 4 - 0 !
src/phasedstacks.cc | 6 3 + 3 - 0 !
src/populations.cc | 8 4 + 4 - 0 !
src/process_shortreads.cc | 4 2 + 2 - 0 !
src/sstacks.cc | 2 1 + 1 - 0 !
src/ustacks.cc | 6 3 + 3 - 0 !
8 files changed, 20 insertions(+), 20 deletions(-)

 fix spelling errors in various generated binaries

scripts/denovo_map.pl | 6 3 + 3 - 0 !
scripts/ref_map.pl | 6 3 + 3 - 0 !
scripts/stacks-gdb | 4 2 + 2 - 0 !
scripts/stacks-samtools-tview | 6 3 + 3 - 0 !
src/clone_filter.cc | 8 4 + 4 - 0 !
src/cstacks.cc | 8 4 + 4 - 0 !
src/kmer_filter.cc | 8 4 + 4 - 0 !
src/phasedstacks.cc | 8 4 + 4 - 0 !
src/populations.cc | 2 1 + 1 - 0 !
src/process_radtags.cc | 20 10 + 10 - 0 !
src/process_shortreads.cc | 8 4 + 4 - 0 !
src/sstacks.cc | 10 5 + 5 - 0 !
src/ustacks.cc | 8 4 + 4 - 0 !
13 files changed, 51 insertions(+), 51 deletions(-)

 fix exit codes to be successful and output to stdout.

scripts/stacks-gdb | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 offer help option