debian/changelog

+gffread (0.11.5-1) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * New upstream release.
+  * Add breaks/replaces on cufflinks (<< 2.2.1+dfsg.1-4). (Closes: #940915)
+  * Set upstream metadata fields: Name.
+
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Wed, 25 Sep 2019 09:15:58 +0200
+
 gffread (0.11.4-2) unstable; urgency=medium
 
   [ Helmut Grohne ]

debian/control

@@ -14,6 +14,8 @@ Package: gffread
 Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends}
+Breaks: cufflinks (<< 2.2.1+dfsg.1-4)
+Replaces: cufflinks (<< 2.2.1+dfsg.1-4)
 Description: GFF/GTF format conversions, region filtering, FASTA sequence extraction
  Gffread is a GFF/GTF parsing utility providing format conversions,
  region filtering, FASTA sequence extraction and more.

debian/patches/gclib.patch

@@ -2,9 +2,9 @@ Author: Andreas Tille <tille@debian.org>
 Last-Update: Thu, 18 Apr 2019 12:40:25 +0200
 Description: Fix build against libgclib
 
---- a/Makefile
-+++ b/Makefile
-@@ -82,8 +82,8 @@ gffread.o : gff_utils.h $(GCLDIR)/GBase.
+--- gffread.orig/Makefile
++++ gffread/Makefile
+@@ -83,8 +83,8 @@
  gff_utils.o : gff_utils.h $(GCLDIR)/gff.h
  ${GCLDIR}/gff.o : ${GCLDIR}/gff.h ${GCLDIR}/GFaSeqGet.h ${GCLDIR}/GList.hh ${GCLDIR}/GHash.hh
  ${GCLDIR}/GFaSeqGet.o : ${GCLDIR}/GFaSeqGet.h

debian/patches/hardening

+From: Michael R. Crusoe <michael.crusoe@gmail.com>
+Subject: Use CPPFLAGS
+
+Allows Debian to harden the binary with CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2
+--- gffread.orig/Makefile
++++ gffread/Makefile
+@@ -65,7 +65,7 @@
+ #endif
+ 
+ %.o : %.cpp
+-	${CXX} ${CXXFLAGS} -c $< -o $@
++	${CXX} ${CPPFLAGS} ${CXXFLAGS} -c $< -o $@
+ 
+ # C/C++ linker
+ 

debian/patches/series

 gclib.patch
+hardening

debian/upstream/metadata

@@ -3,3 +3,4 @@ Registry:
   Entry: OMICS_28050
 - Name: conda:bioconda
   Entry: gffread
+Name: gffread

gffread.cpp

@@ -4,7 +4,7 @@
 #define __STDC_FORMAT_MACROS
 #include <inttypes.h>
 
-#define VERSION "0.11.4"
+#define VERSION "0.11.5"
 
 #define USAGE "gffread v" VERSION ". Usage:\n\
 gffread <input_gff> [-g <genomic_seqs_fasta> | <dir>][-s <seq_info.fsize>] \n\
@@ -1212,7 +1212,7 @@ int main(int argc, char* argv[]) {
  openfw(f_x, args, 'x');
  openfw(f_y, args, 'y');
 
- if (f_out==NULL && f_w==NULL && f_x==NULL && f_y==NULL)
+ if (f_out==NULL && f_w==NULL && f_x==NULL && f_y==NULL && !covInfo)
 	 f_out=stdout;
  //if (f_y!=NULL || f_x!=NULL) wCDSonly=true;
  //useBadCDS=useBadCDS || (fgtfok==NULL && fgtfbad==NULL && f_y==NULL && f_x==NULL);