debian/changelog

+soapaligner (2.20-3) unstable; urgency=medium
+
+  * Team upload.
+  * Architecture: any-amd64 x32
+    Closes: #903003
+  * More sensible date for reproducible builds (SOURCE_DATE_EPOCH)
+  * Force propagation of hardening options
+  * Fix spelling
+
+ -- Andreas Tille <tille@debian.org>  Thu, 05 Jul 2018 13:51:03 +0200
+
 soapaligner (2.20-2) unstable; urgency=medium
 
   * Team upload.

debian/control

@@ -10,7 +10,7 @@ Vcs-Git: https://salsa.debian.org/med-team/soapaligner.git
 Homepage: http://soap.genomics.org.cn/soapaligner.html
 
 Package: soapaligner
-Architecture: any
+Architecture: any-amd64 x32
 Depends: ${shlibs:Depends},
          ${misc:Depends}
 Description: aligner of short reads of next generation sequencers

debian/patches/linkerror.patch

@@ -2,11 +2,9 @@ Author: Steffen Moeller
 Last-Update: 2018-05-04 18:33:03 +0200
 Description: Fix build
 
-Index: soapaligner/Makefile
-===================================================================
---- soapaligner.orig/Makefile
-+++ soapaligner/Makefile
-@@ -32,8 +32,8 @@ ifeq (YES, $(PROFILE))
+--- a/Makefile
++++ b/Makefile
+@@ -37,8 +37,8 @@ ifeq (YES, $(PROFILE))
         CFLAGS += $(PROFILE_FLAGS)
  endif
  
@@ -17,16 +15,14 @@ Index: soapaligner/Makefile
  .SUFFIX: .c .o
  
  .c.o:
-@@ -65,3 +65,5 @@ kstring.o:kstring.h
+@@ -70,3 +70,5 @@ kstring.o:kstring.h
  
  clean:
  	rm -f *.o $(PROG)
 +
 +.PHONY: clean
-Index: soapaligner/Match.c
-===================================================================
---- soapaligner.orig/Match.c
-+++ soapaligner/Match.c
+--- a/Match.c
++++ b/Match.c
 @@ -74,7 +74,8 @@
  	}			\
  }

debian/patches/series

 compiler_options.patch
 linkerror.patch
 UsageDoublette.patch
+spelling.patch

debian/patches/spelling.patch

+Description: Fix spelling
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Thu, 05 Jul 2018 13:04:29 +0200
+
+--- a/soap.1
++++ b/soap.1
+@@ -69,7 +69,7 @@ Totally allowed mismatches in one read,
+ Allow gap size in one read, [0]
+ .TP
+ .B -M INT
+-Match mode for each read or the seed part of read, which shouldn't contain more than 2 mismaches, [4]
++Match mode for each read or the seed part of read, which shouldn't contain more than 2 mismatches, [4]
+ .RS
+ .TP
+ 0: exact match only
+@@ -88,7 +88,7 @@ SOAP2 output format contains following c
+ .PP
+ 1. reads name / reads ID (if -t is available)
+ .P
+-2. reads sequence (if read align to reverse strand, here is the reverse sequence of orignal read)
++2. reads sequence (if read align to reverse strand, here is the reverse sequence of original read)
+ .P
+ 3. quality sequence (if input is fasta reads, the column will be all 'h', and the sequence is backward if reads mapping reverse )
+ .P
+--- a/soap.c
++++ b/soap.c
+@@ -119,7 +119,7 @@ static void Usage(void) {
+ 	fprintf(stdout,	"\t-b  <str>   query b file\n");
+ 	fprintf(stdout,	"\t-D  <str>   reference sequences indexing table, *.index format\n");
+ 	fprintf(stdout,	"\t-o  <str>   output alignment file(txt)\n");
+-	fprintf(stdout, "\t-M  <int>   match mode for each read or the seed part of read, which shouldn't contain more than 2 mismaches, [4]\n"
++	fprintf(stdout, "\t-M  <int>   match mode for each read or the seed part of read, which shouldn't contain more than 2 mismatches, [4]\n"
+ 			"\t            0: exact match only\n"
+ 			"\t            1: 1 mismatch match only\n"
+ 			"\t            2: 2 mismatch match only\n"
+--- a/soap.man
++++ b/soap.man
+@@ -71,7 +71,7 @@ CCOOMMMMAANNDD AANNDD OOPPT
+               --gg IINNTT Allow gap size in one read, [0]
+ 
+               --MM IINNTT Match mode for each read or the seed part of read,  which
+-                     shouldn't contain more than 2 mismaches, [4]
++                     shouldn't contain more than 2 mismatches, [4]
+ 
+                      0: exact match only
+ 

debian/rules

@@ -2,14 +2,13 @@
 # -*- makefile -*-
 
 # Uncomment this to turn on verbose mode.
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 export DH_VERBOSE=1
-export DFLAGS = -DMAKE_TIME=\""be reproducible"\"
-
-export CFLAGS += -flto
-export CXXFLAGS += -flto
-export LDFLAGS += -Wl,-flto
+export DFLAGS = -DMAKE_TIME=\""SOURCE_DATE_EPOCH"\"
 
-export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+export CFLAGS:=-flto $(shell dpkg-buildflags --get CFLAGS)
+export CXXFLAGS:=-flto $(shell dpkg-buildflags --get CXXFLAGS)
+export LDFLAGS:=-Wl,-flto $(shell dpkg-buildflags --get LDFLAGS)
 
 %:
 	dh $@