src/gff2aplot.pl | 19 10 9 - 0 !
1 file changed, 10 insertions( ), 9 deletions(-)

 make sure that iterator variable is explicitly decalred as
 a lexcical using my keyword. See PBP, page 108.  Add perl shebang.

src/blat2gff.pl | 8 4 4 - 0 !
1 file changed, 4 insertions( ), 4 deletions(-)

---

src/parseblast.pl | 4 2 2 - 0 !
1 file changed, 2 insertions( ), 2 deletions(-)

---

src/ali2gff/Makefile | 2 1 1 - 0 !
1 file changed, 1 insertion( ), 1 deletion(-)

 use build flags from environment (dpkg-buildflags).
 Necessary for hardening flags.

src/ali2gff/ali2gff.c | 10 7 3 - 0 !
1 file changed, 7 insertions( ), 3 deletions(-)

 deal with mayhem issue

examples/mhcregion/index.html | 30 15 15 - 0 !
examples/wublast/index.html | 30 15 15 - 0 !
2 files changed, 30 insertions( ), 30 deletions(-)

 fix privacy issues by linking to local images, js and css locally

src/gff2aplot.pl | 13 9 4 - 0 !
1 file changed, 9 insertions( ), 4 deletions(-)

 can't use 'defined(@array)' (maybe you should just omit the defined()?) at /usr/bin/gff2aplot line 1737.

Makefile | 5 3 2 - 0 !
1 file changed, 3 insertions( ), 2 deletions(-)

 make sure target dir exists when performing parallel builds
 Somehow CP is resolved to "cp 1" - no idea why, just force proper copy statement

src/ali2gff/ali2gff.c | 10 5 5 - 0 !
1 file changed, 5 insertions( ), 5 deletions(-)

 enhance print buffer to avoid:
  /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 36 and 3418 bytes into a destination of size 1000
 Finally this patch is not fully working since the enhanced buffers
 make sprint assume that even larger buffers are needed.

examples/splice_sites/README | 3 1 2 - 0 !
1 file changed, 1 insertion( ), 2 deletions(-)

 the readme file is used as shell script and one function
 is broken.  It should return basenames of *.ps files.  This is fixed here

examples/mhcregion/hs-mm.gff | 2 1 1 - 0 !
examples/mhcregion/hs-mm.sim.gff | 2 1 1 - 0 !
2 files changed, 2 insertions( ), 2 deletions(-)

 replace tabs in gff files with spaces
 GFFparsers are supposed to ignore all the text in lines that start with # but 
 for some reason, gffread doesn't like tabs in comments.
 The number of tabs after which gffread complains seems to be related to the 
 following line, but since this is just a comment anyway, replacing tabs with
 spaces seems like an easier fix.