Preparations for initial upload.

soapaligner (2.20-1) UNRELEASED; urgency=low

soapaligner (2.20-1) unstable; urgency=low

  [ Steffen Moeller ]

  * Initial release (Closes: #669917)

  * Initial release (Closes: #669917,#897908)

    There is a version 2.21 released as a binary for

    which I failed to find the source code.

  [ Andreas Tille ]

  * Moved packaging from SVN to Git

Section: science

Priority: optional

Build-Depends: debhelper (>= 10)

Standards-Version: 4.1.1

Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/soapaligner.git

Vcs-Git: https://anonscm.debian.org/git/debian-med/soapaligner.git

Standards-Version: 4.1.3

Vcs-Browser: https://salsa.debian.org/med-team/soapaligner

Vcs-Git: https://salsa.debian.org/med-team/soapaligner.git

Homepage: http://soap.genomics.org.cn/soapaligner.html

Package: soapaligner

Index: soapaligner/soap.c

===================================================================

--- soapaligner.orig/soap.c

+++ soapaligner/soap.c

@@ -107,7 +107,7 @@ unsigned char complementMap[256];

 static SOAPOPT *opt;

-void Usage(void) {

+static void Usage(void) {

 	fprintf(stdout, "\nProgram: %s\n", PROGRAM);

 	fprintf(stdout, "Compile Date: "

 			MAKE_TIME"\n");

Index: soap2-2.20/Makefile

Index: soapaligner/Makefile

===================================================================

--- soap2-2.20.orig/Makefile	2009-07-23 00:49:31.000000000 +0200

+++ soap2-2.20/Makefile	2012-04-22 00:01:01.446041368 +0200

@@ -6,7 +6,7 @@

 CC            = gcc

 DEBUG_FLAGS   = -g3 -Wall -O2

 PROFILE_FLAGS = -fprofile-arcs -ftest-coverage -pg 

--- soapaligner.orig/Makefile

+++ soapaligner/Makefile

@@ -1,33 +1,40 @@

-SHELL         = /bin/sh

-PROG          = soap

-DEBUG         = NO

-PROFILE       = NO

-PTHREADS      = YES

-CC            = gcc

-DEBUG_FLAGS   = -g3 -Wall -O2

-PROFILE_FLAGS = -fprofile-arcs -ftest-coverage -pg 

-RELEASE_FLAGS = -msse3 -O3 -static -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer 

+RELEASE_FLAGS = $(DEBUG_FLAGS)

 STATIC_FLAGS  = -static

 DFLAGS        = -DMAKE_TIME=\""`date`"\"

 LIBS          = -lm

@@ -18,7 +18,7 @@

         DFLAGS  += -DDEBUG

-STATIC_FLAGS  = -static

-DFLAGS        = -DMAKE_TIME=\""`date`"\"

-LIBS          = -lm

+SHELL         ?= /bin/sh

+PROG          ?= soap

+DEBUG         ?= NO

+STATIC        ?= NO

+PROFILE       ?= NO

+PTHREADS      ?= YES

+CC            ?= gcc

+DEBUG_FLAGS   ?= -g3 -Wall -O2

+PROFILE_FLAGS ?= -fprofile-arcs -ftest-coverage -pg

+RELEASE_FLAGS ?= -msse3 -O3 -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer

+STATIC_FLAGS  ?= -static

+DFLAGS        ?= -DMAKE_TIME=\""`date`"\"

+LDFLAGS       ?=

+LIBS          ?= -lm

 #TARBALL_EXCLUDE = "*.(o,gz,zip)"

 #ZIP_EXCLUDE     = *.o *.gz *.zip

+ifeq (YES, $(STATIC))

+	CFLAGS += $(STATIC_FLAGS)

+endif

+

 ifeq (YES, $(DEBUG))

-        CFLAGS   = $(DEBUG_FLAGS) $(STATIC_FLAGS)

-        DFLAGS  += -DDEBUG

+        CFLAGS  += $(DEBUG_FLAGS) $(STATIC_FLAGS)

+        CFLAGS  += -DDEBUG

 #        PTHREADS = NO

 else

-        CFLAGS   = $(RELEASE_FLAGS) $(STATIC_FLAGS)

+        CFLAGS   = $(RELEASE_FLAGS)

+        CFLAGS  += $(RELEASE_FLAGS)

 endif

 ifeq (YES, $(PTHREADS))

         LIBS   +=  -lpthread

-        DFLAGS +=  -DPTHREADS

+        CFLAGS +=  -DPTHREADS

 endif

+CFLAGS += $(DFLAGS)

 ifeq (YES, $(PROFILE))

-       DFLAGS += $(PROFILE_FLAGS)

+       CFLAGS += $(PROFILE_FLAGS)

 endif

 OBJ = SeqIO.o MiscUtilities.o MemManager.o TextConverter.o r250.o DNACount.o HSP.o Timing.o BWT.o extratools.o soapio.o BWTAln.o Match.o PairMatch.o stdaln.o kstring.o

@@ -35,12 +42,12 @@ OBJ = SeqIO.o MiscUtilities.o MemManager

 .SUFFIX: .c .o

 .c.o:

-	$(CC) -c $(CFLAGS) $(DFLAGS) $< -o $@

+	$(CC) -c $(CFLAGS) $< -o $@

 all: $(PROG)

-$(PROG): $(OBJ) soap.o

-	$(CC) $(CFLAGS) $(DFLAGS) $(OBJ) soap.o -o $@ $(LIBS)

+$(PROG): $(OBJ)

+	$(CC) $(CFLAGS) $(OBJ) -o $@ $(LDFLAGS) $(LIBS)

 SeqIO.o:SeqIO.h

 r250.o: r250.h

Index: soapaligner/Makefile

===================================================================

--- soapaligner.orig/Makefile

+++ soapaligner/Makefile

@@ -32,8 +32,8 @@ ifeq (YES, $(PROFILE))

        CFLAGS += $(PROFILE_FLAGS)

 endif

-OBJ = SeqIO.o MiscUtilities.o MemManager.o TextConverter.o r250.o DNACount.o HSP.o Timing.o BWT.o extratools.o soapio.o BWTAln.o Match.o PairMatch.o stdaln.o kstring.o

-.SUFFIX:

+OBJ = SeqIO.o MiscUtilities.o MemManager.o TextConverter.o r250.o DNACount.o HSP.o Timing.o BWT.o extratools.o soapio.o BWTAln.o Match.o PairMatch.o stdaln.o kstring.o soap.o

+

 .SUFFIX: .c .o

 .c.o:

@@ -65,3 +65,5 @@ kstring.o:kstring.h

 clean:

 	rm -f *.o $(PROG)

+

+.PHONY: clean

Index: soapaligner/Match.c

===================================================================

--- soapaligner.orig/Match.c

+++ soapaligner/Match.c

@@ -74,7 +74,8 @@

 	}			\

 }

-inline void PickupHit(ALNSEQ *alnSeq, const int rr,int *site, HITTABLE *hits, const unsigned int *pacRef, const unsigned int dnaLength, unsigned short *cigar){

+/*inline */

+void PickupHit(ALNSEQ *alnSeq, const int rr,int *site, HITTABLE *hits, const unsigned int *pacRef, const unsigned int dnaLength, unsigned short *cigar){

 #ifdef DEBUG

 //		fprintf(stderr, "Pick up for output\n");

 #endif