[med-svn] [freebayes] 03/06: Changes to build new upstream version
Andreas Tille
tille at debian.org
Sat Sep 2 05:46:08 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to tag debian/1.0.2-1
in repository freebayes.
commit dbf514922d3398558c07f383b1cb156d44feda57
Author: Andreas Tille <tille at debian.org>
Date: Sun Jun 18 14:51:22 2017 +0200
Changes to build new upstream version
---
debian/README.source | 11 +
debian/changelog | 6 +
debian/control | 9 +-
debian/copyright | 428 +--------------------
debian/patches/fix_test.patch | 8 +
debian/patches/series | 3 +
debian/patches/use_debian_packaged_bamtools.patch | 68 ++--
.../patches/use_debian_packaged_libjsoncpp.patch | 17 +
debian/patches/use_debian_packaged_seqlib.patch | 87 +++++
debian/patches/use_debian_packaged_vcflib.patch | 271 ++-----------
debian/patches/vcffirstheader.patch | 29 ++
debian/rules | 6 +-
debian/test-simple-bash/lib/test-simple.bash | 110 ++++++
debian/test-simple-bash/test/basics.t | 26 ++
debian/test-simple-bash/test/doc.t | 15 +
debian/test-simple-bash/test/no-label.t | 25 ++
16 files changed, 416 insertions(+), 703 deletions(-)
diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..26e4dc4
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,11 @@
+To run the test suite some bash testing framework was used
+bu upstream as Git submodules. For the Git packaging these
+were downloaded separately
+
+Files: debian/bash-tap/*
+ Obtained from
+ https://github.com/illusori/bash-tap
+
+Files: debian/test-simple-bash/*
+ Obtained from
+ https://github.com/ingydotnet/test-simple-bash/tree/master/lib
diff --git a/debian/changelog b/debian/changelog
index eaeaad5..4fec7a2 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+freebayes (1.1.0-1) UNRELEASED; urgency=medium
+
+ * New upstream version
+
+ -- Andreas Tille <tille at debian.org> Sun, 18 Jun 2017 14:47:55 +0200
+
freebayes (1.0.2-1) unstable; urgency=low
* Initial packaging (Closes: #851306)
diff --git a/debian/control b/debian/control
index 301577b..99d8397 100644
--- a/debian/control
+++ b/debian/control
@@ -7,12 +7,16 @@ Priority: optional
Build-Depends: debhelper (>= 9),
cmake,
pkg-config,
+ python,
zlib1g-dev,
libbamtools-dev,
- libvcflib-dev,
+ libvcflib-dev (>= 1.0.0~rc1+dfsg1-4),
libtabixpp-dev,
+ libseqlib-dev,
bc,
- samtools
+ samtools,
+ parallel,
+ libvcflib-tools
Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/freebayes.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/freebayes.git
@@ -22,6 +26,7 @@ Package: freebayes
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends}
+Recommends: parallel
Description: Bayesian haplotype-based polymorphism discovery and genotyping
FreeBayes is a Bayesian genetic variant detector designed to find
small polymorphisms, specifically SNPs (single-nucleotide
diff --git a/debian/copyright b/debian/copyright
index 06830b0..6a31d5e 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -9,6 +9,14 @@ License: MIT
Files: debian/bash-tap/*
Copyright: 2012-2016 Sam Graham
License: MIT
+Comment: Files obtained from
+ https://github.com/illusori/bash-tap
+
+Files: debian/test-simple-bash
+Copyright: 2013 Ingy.Net
+License: MIT
+Comment: File obtained from
+ https://github.com/ingydotnet/test-simple-bash/tree/master/lib
Files: ttmath/*
Copyright: 2006-2012, Tomasz Sowa
@@ -39,426 +47,6 @@ License: BSD-3-clause
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
THE POSSIBILITY OF SUCH DAMAGE.
-Files: src/fastlz.*
-Copyright: 2005-2007 Ariya Hidayat <ariya at kde.org>
-License: MIT
-
-Files: paper/genome_research.bst
-Copyright: 1994-2007 Patrick W Daly
-License: LPPL-1+
- The LaTeX Project Public License
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Files: debian/*
Copyright: 2014 Brad Chapman <chapmanb at 50mail.com>
License: MIT
diff --git a/debian/patches/fix_test.patch b/debian/patches/fix_test.patch
index a5af80c..302ed80 100644
--- a/debian/patches/fix_test.patch
+++ b/debian/patches/fix_test.patch
@@ -13,3 +13,11 @@ Description: vcflib is in a different package - do not test this
prove -v t
$(freebayes):
+--- a/scripts/freebayes-parallel
++++ b/scripts/freebayes-parallel
+@@ -37,4 +37,4 @@ command=("freebayes" "$@")
+ # iterate over regions using gnu parallel to dispatch jobs
+ cat "$regionsfile" | parallel -k -j "$ncpus" "${command[@]}" --region {}
+ ) | ../vcflib/scripts/vcffirstheader \
+- | ../vcflib/bin/vcfstreamsort -w 1000 | vcfuniq # remove duplicates at region edges
++ | vcfstreamsort -w 1000 | vcfuniq # remove duplicates at region edges
diff --git a/debian/patches/series b/debian/patches/series
index e9ae68a..3052e50 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,6 @@
use_debian_packaged_bamtools.patch
use_debian_packaged_vcflib.patch
+use_debian_packaged_seqlib.patch
+use_debian_packaged_libjsoncpp.patch
fix_test.patch
+vcffirstheader.patch
diff --git a/debian/patches/use_debian_packaged_bamtools.patch b/debian/patches/use_debian_packaged_bamtools.patch
index 23f035e..9155580 100644
--- a/debian/patches/use_debian_packaged_bamtools.patch
+++ b/debian/patches/use_debian_packaged_bamtools.patch
@@ -4,83 +4,83 @@ Description: Use Debian packaged bamtools
--- a/src/Makefile
+++ b/src/Makefile
-@@ -12,11 +12,10 @@ C=gcc
+@@ -12,14 +12,13 @@ C=gcc
CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g
#CFLAGS=-O3 -static -D VERBOSE_DEBUG # enables verbose debugging via --debug2
-BAMTOOLS_ROOT=../bamtools
+ SEQLIB_ROOT=../SeqLib
VCFLIB_ROOT=../vcflib
+ TABIX_ROOT=$(VCFLIB_ROOT)/tabixpp
+ HTSLIB_ROOT=$(TABIX_ROOT)/htslib
--LIBS = -L./ -L$(VCFLIB_ROOT)/tabixpp/ -L$(BAMTOOLS_ROOT)/lib -ltabix -lz -lm
--INCLUDE = -I$(BAMTOOLS_ROOT)/src -I../ttmath -I$(VCFLIB_ROOT)/src -I$(VCFLIB_ROOT)/
-+LIBS = -L./ -L$(VCFLIB_ROOT)/tabixpp/ -lbamtools -ltabixpp -lz -lm
-+INCLUDE = -I/usr/include/bamtools -I../ttmath -I$(VCFLIB_ROOT)/src -I$(VCFLIB_ROOT)/
+-LIBS = -lz -lm -lpthread
+-INCLUDE = -I../ttmath -I$(BAMTOOLS_ROOT)/src/ -I$(VCFLIB_ROOT)/src/ -I$(TABIX_ROOT)/ -I$(VCFLIB_ROOT)/smithwaterman/ -I$(VCFLIB_ROOT)/multichoose/ -I$(VCFLIB_ROOT)/filevercmp/ -I$(HTSLIB_ROOT) -I$(SEQLIB_ROOT) -I$(SEQLIB_ROOT)/htslib
++LIBS = -lbamtools -ltabixpp -lz -lm -lpthread
++INCLUDE = -I../ttmath -I/usr/include/bamtools -I$(VCFLIB_ROOT)/src/ -I$(TABIX_ROOT)/ -I$(VCFLIB_ROOT)/smithwaterman/ -I$(VCFLIB_ROOT)/multichoose/ -I$(VCFLIB_ROOT)/filevercmp/ -I$(HTSLIB_ROOT) -I$(SEQLIB_ROOT) -I$(SEQLIB_ROOT)/htslib
all: autoversion ../bin/freebayes ../bin/bamleftalign
-@@ -34,10 +33,6 @@ gprof:
+@@ -37,9 +36,6 @@ gprof:
.PHONY: all static debug profiling gprof
-# builds bamtools static lib, and copies into root
-$(BAMTOOLS_ROOT)/lib/libbamtools.a:
- cd $(BAMTOOLS_ROOT) && mkdir -p build && cd build && cmake .. && $(MAKE)
--
+ $(HTSLIB_ROOT)/libhts.a:
+ cd $(HTSLIB_ROOT) && make
- OBJECTS=BedReader.o \
- CNV.o \
-@@ -70,8 +65,7 @@ OBJECTS=BedReader.o \
- ../vcflib/smithwaterman/LeftAlign.o \
+@@ -78,7 +74,6 @@ OBJECTS=BedReader.o \
../vcflib/smithwaterman/Repeats.o \
../vcflib/smithwaterman/IndelAllele.o \
-- Variant.o \
-- $(BAMTOOLS_ROOT)/lib/libbamtools.a
-+ Variant.o
-
- HEADERS=multichoose.h version_git.h
-
-@@ -86,10 +80,10 @@ alleles ../bin/alleles: alleles.o $(OBJE
+ Variant.o \
+- $(BAMTOOLS_ROOT)/lib/libbamtools.a \
+ $(SEQLIB_ROOT)/src/libseqlib.a \
+ $(SEQLIB_ROOT)/bwa/libbwa.a \
+ $(SEQLIB_ROOT)/fermi-lite/libfml.a \
+@@ -97,10 +92,10 @@ alleles ../bin/alleles: alleles.o $(OBJE
dummy ../bin/dummy: dummy.o $(OBJECTS) $(HEADERS)
$(CXX) $(CFLAGS) $(INCLUDE) dummy.o $(OBJECTS) -o ../bin/dummy $(LIBS)
--bamleftalign ../bin/bamleftalign: $(BAMTOOLS_ROOT)/lib/libbamtools.a bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o
-- $(CXX) $(CFLAGS) $(INCLUDE) bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o $(BAMTOOLS_ROOT)/lib/libbamtools.a -o ../bin/bamleftalign $(LIBS)
-+bamleftalign ../bin/bamleftalign: bamleftalign.o Fasta.o
-+ $(CXX) $(CFLAGS) $(INCLUDE) bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o -o ../bin/bamleftalign -lbamtools
+-bamleftalign ../bin/bamleftalign: $(BAMTOOLS_ROOT)/lib/libbamtools.a $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o
+- $(CXX) $(CFLAGS) $(INCLUDE) bamleftalign.o Fasta.o Utility.o LeftAlign.o IndelAllele.o split.o $(BAMTOOLS_ROOT)/lib/libbamtools.a $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a -o ../bin/bamleftalign $(LIBS)
++bamleftalign ../bin/bamleftalign: $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o
++ $(CXX) $(CFLAGS) $(INCLUDE) bamleftalign.o Fasta.o Utility.o LeftAlign.o IndelAllele.o split.o $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a -o ../bin/bamleftalign $(LIBS)
--bamfiltertech ../bin/bamfiltertech: $(BAMTOOLS_ROOT)/lib/libbamtools.a bamfiltertech.o $(OBJECTS) $(HEADERS)
-+bamfiltertech ../bin/bamfiltertech: bamfiltertech.o $(OBJECTS) $(HEADERS)
+-bamfiltertech ../bin/bamfiltertech: $(BAMTOOLS_ROOT)/lib/libbamtools.a $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a bamfiltertech.o $(OBJECTS) $(HEADERS)
++bamfiltertech ../bin/bamfiltertech: $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a bamfiltertech.o $(OBJECTS) $(HEADERS)
$(CXX) $(CFLAGS) $(INCLUDE) bamfiltertech.o $(OBJECTS) -o ../bin/bamfiltertech $(LIBS)
-@@ -104,7 +98,7 @@ alleles.o: alleles.cpp AlleleParser.o Al
+@@ -115,7 +110,7 @@ alleles.o: alleles.cpp AlleleParser.o Al
dummy.o: dummy.cpp AlleleParser.o Allele.o
$(CXX) $(CFLAGS) $(INCLUDE) -c dummy.cpp
--freebayes.o: freebayes.cpp TryCatch.h $(BAMTOOLS_ROOT)/lib/libbamtools.a
-+freebayes.o: freebayes.cpp TryCatch.h
+-freebayes.o: freebayes.cpp TryCatch.h $(HTSLIB_ROOT)/libhts.a $(BAMTOOLS_ROOT)/lib/libbamtools.a
++freebayes.o: freebayes.cpp TryCatch.h $(HTSLIB_ROOT)/libhts.a
$(CXX) $(CFLAGS) $(INCLUDE) -c freebayes.cpp
fastlz.o: fastlz.c fastlz.h
-@@ -125,7 +119,7 @@ Genotype.o: Genotype.cpp Genotype.h Alle
+@@ -136,7 +131,7 @@ Genotype.o: Genotype.cpp Genotype.h Alle
Ewens.o: Ewens.cpp Ewens.h
$(CXX) $(CFLAGS) $(INCLUDE) -c Ewens.cpp
--AlleleParser.o: AlleleParser.cpp AlleleParser.h multichoose.h Parameters.h $(BAMTOOLS_ROOT)/lib/libbamtools.a
-+AlleleParser.o: AlleleParser.cpp AlleleParser.h multichoose.h Parameters.h
+-AlleleParser.o: AlleleParser.cpp AlleleParser.h multichoose.h Parameters.h $(BAMTOOLS_ROOT)/lib/libbamtools.a $(HTSLIB_ROOT)/libhts.a
++AlleleParser.o: AlleleParser.cpp AlleleParser.h multichoose.h Parameters.h $(HTSLIB_ROOT)/libhts.a
$(CXX) $(CFLAGS) $(INCLUDE) -c AlleleParser.cpp
Utility.o: Utility.cpp Utility.h Sum.h Product.h
-@@ -173,7 +167,7 @@ bamleftalign.o: bamleftalign.cpp LeftAli
+@@ -184,7 +179,7 @@ bamleftalign.o: bamleftalign.cpp LeftAli
bamfiltertech.o: bamfiltertech.cpp
$(CXX) $(CFLAGS) $(INCLUDE) -c bamfiltertech.cpp
--LeftAlign.o: LeftAlign.h LeftAlign.cpp $(BAMTOOLS_ROOT)/lib/libbamtools.a
-+LeftAlign.o: LeftAlign.h LeftAlign.cpp
+-LeftAlign.o: LeftAlign.h LeftAlign.cpp $(BAMTOOLS_ROOT)/lib/libbamtools.a $(HTSLIB_ROOT)/libhts.a
++LeftAlign.o: LeftAlign.h LeftAlign.cpp $(HTSLIB_ROOT)/libhts.a
$(CXX) $(CFLAGS) $(INCLUDE) -c LeftAlign.cpp
IndelAllele.o: IndelAllele.cpp IndelAllele.h
-@@ -263,6 +257,5 @@ autoversion:
+@@ -275,6 +270,5 @@ autoversion:
clean:
rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a}
diff --git a/debian/patches/use_debian_packaged_libjsoncpp.patch b/debian/patches/use_debian_packaged_libjsoncpp.patch
new file mode 100644
index 0000000..5ded25a
--- /dev/null
+++ b/debian/patches/use_debian_packaged_libjsoncpp.patch
@@ -0,0 +1,17 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 28 May 2014 21:23:38 +0200
+Description: Use Debian packaged libjsoncpp
+
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -12,8 +12,8 @@ C=gcc
+ CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g
+ #CFLAGS=-O3 -static -D VERBOSE_DEBUG # enables verbose debugging via --debug2
+
+-LIBS = -lbamtools -ltabixpp -lz -lm -lpthread `pkg-config --libs libvcflib` `pkg-config --libs htslib` `pkg-config --libs libseqlib`
+-INCLUDE = -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib`
++LIBS = -lbamtools -ltabixpp -lz -lm -lpthread `pkg-config --libs libvcflib` `pkg-config --libs htslib` `pkg-config --libs libseqlib` `pkg-config --libs jsoncpp`
++INCLUDE = -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp`
+
+ all: autoversion ../bin/freebayes ../bin/bamleftalign
+
diff --git a/debian/patches/use_debian_packaged_seqlib.patch b/debian/patches/use_debian_packaged_seqlib.patch
new file mode 100644
index 0000000..9e7a35b
--- /dev/null
+++ b/debian/patches/use_debian_packaged_seqlib.patch
@@ -0,0 +1,87 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 28 May 2014 21:23:38 +0200
+Description: Use Debian packaged htslib and seqlib
+ seqlib carries another copy of htslib - we replace both
+
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -12,10 +12,8 @@ C=gcc
+ CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g
+ #CFLAGS=-O3 -static -D VERBOSE_DEBUG # enables verbose debugging via --debug2
+
+-SEQLIB_ROOT=../SeqLib
+-
+-LIBS = -lbamtools -ltabixpp -lz -lm -lpthread `pkg-config --libs libvcflib`
+-INCLUDE = -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` -I$(SEQLIB_ROOT) -I$(SEQLIB_ROOT)/htslib
++LIBS = -lbamtools -ltabixpp -lz -lm -lpthread `pkg-config --libs libvcflib` `pkg-config --libs htslib` `pkg-config --libs libseqlib`
++INCLUDE = -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib`
+
+ all: autoversion ../bin/freebayes ../bin/bamleftalign
+
+@@ -33,12 +31,6 @@ gprof:
+
+ .PHONY: all static debug profiling gprof
+
+-$(HTSLIB_ROOT)/libhts.a:
+- cd $(HTSLIB_ROOT) && make
+-
+-$(SEQLIB_ROOT)/src/libseqlib.a:
+- cd $(SEQLIB_ROOT) && ./configure && make
+-
+ OBJECTS=BedReader.o \
+ CNV.o \
+ fastlz.o \
+@@ -62,11 +54,7 @@ OBJECTS=BedReader.o \
+ Bias.o \
+ Contamination.o \
+ NonCall.o \
+- SegfaultHandler.o \
+- $(SEQLIB_ROOT)/src/libseqlib.a \
+- $(SEQLIB_ROOT)/bwa/libbwa.a \
+- $(SEQLIB_ROOT)/fermi-lite/libfml.a \
+- $(SEQLIB_ROOT)/htslib/libhts.a
++ SegfaultHandler.o
+
+ HEADERS=multichoose.h version_git.h
+
+@@ -81,10 +69,10 @@ alleles ../bin/alleles: alleles.o $(OBJE
+ dummy ../bin/dummy: dummy.o $(OBJECTS) $(HEADERS)
+ $(CXX) $(CFLAGS) $(INCLUDE) dummy.o $(OBJECTS) -o ../bin/dummy $(LIBS)
+
+-bamleftalign ../bin/bamleftalign: $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o
+- $(CXX) $(CFLAGS) $(INCLUDE) bamleftalign.o Fasta.o Utility.o LeftAlign.o IndelAllele.o split.o $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a -o ../bin/bamleftalign $(LIBS)
++bamleftalign ../bin/bamleftalign: bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o
++ $(CXX) $(CFLAGS) $(INCLUDE) bamleftalign.o Fasta.o Utility.o LeftAlign.o IndelAllele.o split.o -o ../bin/bamleftalign $(LIBS)
+
+-bamfiltertech ../bin/bamfiltertech: $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a bamfiltertech.o $(OBJECTS) $(HEADERS)
++bamfiltertech ../bin/bamfiltertech: bamfiltertech.o $(OBJECTS) $(HEADERS)
+ $(CXX) $(CFLAGS) $(INCLUDE) bamfiltertech.o $(OBJECTS) -o ../bin/bamfiltertech $(LIBS)
+
+
+@@ -99,7 +87,7 @@ alleles.o: alleles.cpp AlleleParser.o Al
+ dummy.o: dummy.cpp AlleleParser.o Allele.o
+ $(CXX) $(CFLAGS) $(INCLUDE) -c dummy.cpp
+
+-freebayes.o: freebayes.cpp TryCatch.h $(HTSLIB_ROOT)/libhts.a
++freebayes.o: freebayes.cpp TryCatch.h
+ $(CXX) $(CFLAGS) $(INCLUDE) -c freebayes.cpp
+
+ fastlz.o: fastlz.c fastlz.h
+@@ -120,7 +108,7 @@ Genotype.o: Genotype.cpp Genotype.h Alle
+ Ewens.o: Ewens.cpp Ewens.h
+ $(CXX) $(CFLAGS) $(INCLUDE) -c Ewens.cpp
+
+-AlleleParser.o: AlleleParser.cpp AlleleParser.h multichoose.h Parameters.h $(HTSLIB_ROOT)/libhts.a
++AlleleParser.o: AlleleParser.cpp AlleleParser.h multichoose.h Parameters.h
+ $(CXX) $(CFLAGS) $(INCLUDE) -c AlleleParser.cpp
+
+ Utility.o: Utility.cpp Utility.h Sum.h Product.h
+@@ -168,7 +156,7 @@ bamleftalign.o: bamleftalign.cpp LeftAli
+ bamfiltertech.o: bamfiltertech.cpp
+ $(CXX) $(CFLAGS) $(INCLUDE) -c bamfiltertech.cpp
+
+-LeftAlign.o: LeftAlign.h LeftAlign.cpp $(HTSLIB_ROOT)/libhts.a
++LeftAlign.o: LeftAlign.h LeftAlign.cpp
+ $(CXX) $(CFLAGS) $(INCLUDE) -c LeftAlign.cpp
+
+ IndelAllele.o: IndelAllele.cpp IndelAllele.h
diff --git a/debian/patches/use_debian_packaged_vcflib.patch b/debian/patches/use_debian_packaged_vcflib.patch
index dd907a8..dc36617 100644
--- a/debian/patches/use_debian_packaged_vcflib.patch
+++ b/debian/patches/use_debian_packaged_vcflib.patch
@@ -4,45 +4,46 @@ Description: vcflib needs to be packaged separately
--- a/src/Makefile
+++ b/src/Makefile
-@@ -12,10 +12,8 @@ C=gcc
- CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g
+@@ -13,12 +13,9 @@ CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g
#CFLAGS=-O3 -static -D VERBOSE_DEBUG # enables verbose debugging via --debug2
+ SEQLIB_ROOT=../SeqLib
-VCFLIB_ROOT=../vcflib
--
--LIBS = -L./ -L$(VCFLIB_ROOT)/tabixpp/ -lbamtools -ltabixpp -lz -lm
--INCLUDE = -I/usr/include/bamtools -I../ttmath -I$(VCFLIB_ROOT)/src -I$(VCFLIB_ROOT)/
-+LIBS = -lbamtools -ltabixpp -lz -lm -lvcflib `pkg-config --libs libsmithwaterman`
-+INCLUDE = -I/usr/include/bamtools -I../ttmath -I/usr/include/vcflib -I/usr/include/intervaltree `pkg-config --cflags libsmithwaterman` -ldisorder
+-TABIX_ROOT=$(VCFLIB_ROOT)/tabixpp
+-HTSLIB_ROOT=$(TABIX_ROOT)/htslib
+
+-LIBS = -lbamtools -ltabixpp -lz -lm -lpthread
+-INCLUDE = -I../ttmath -I/usr/include/bamtools -I$(VCFLIB_ROOT)/src/ -I$(TABIX_ROOT)/ -I$(VCFLIB_ROOT)/smithwaterman/ -I$(VCFLIB_ROOT)/multichoose/ -I$(VCFLIB_ROOT)/filevercmp/ -I$(HTSLIB_ROOT) -I$(SEQLIB_ROOT) -I$(SEQLIB_ROOT)/htslib
++LIBS = -lbamtools -ltabixpp -lz -lm -lpthread `pkg-config --libs libvcflib`
++INCLUDE = -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` -I$(SEQLIB_ROOT) -I$(SEQLIB_ROOT)/htslib
all: autoversion ../bin/freebayes ../bin/bamleftalign
-@@ -57,15 +55,7 @@ OBJECTS=BedReader.o \
- Bias.o \
+@@ -66,14 +63,6 @@ OBJECTS=BedReader.o \
Contamination.o \
NonCall.o \
-- SegfaultHandler.o \
+ SegfaultHandler.o \
- ../vcflib/tabixpp/tabix.o \
-- ../vcflib/tabixpp/bgzf.o \
+- ../vcflib/tabixpp/htslib/bgzf.o \
- ../vcflib/smithwaterman/SmithWatermanGotoh.o \
-- ../vcflib/smithwaterman/disorder.c \
+- ../vcflib/smithwaterman/disorder.cpp \
- ../vcflib/smithwaterman/LeftAlign.o \
- ../vcflib/smithwaterman/Repeats.o \
- ../vcflib/smithwaterman/IndelAllele.o \
-- Variant.o
-+ SegfaultHandler.o
-
- HEADERS=multichoose.h version_git.h
-
-@@ -173,17 +163,6 @@ LeftAlign.o: LeftAlign.h LeftAlign.cpp
+- Variant.o \
+ $(SEQLIB_ROOT)/src/libseqlib.a \
+ $(SEQLIB_ROOT)/bwa/libbwa.a \
+ $(SEQLIB_ROOT)/fermi-lite/libfml.a \
+@@ -185,18 +174,6 @@ LeftAlign.o: LeftAlign.h LeftAlign.cpp $
IndelAllele.o: IndelAllele.cpp IndelAllele.h
$(CXX) $(CFLAGS) $(INCLUDE) -c IndelAllele.cpp
-Variant.o: $(VCFLIB_ROOT)/src/Variant.h $(VCFLIB_ROOT)/src/Variant.cpp
- $(CXX) $(CFLAGS) $(INCLUDE) -c $(VCFLIB_ROOT)/src/Variant.cpp
-
--../vcflib/tabixpp/tabix.o: ../vcflib/tabixpp/tabix.hpp ../vcflib/tabixpp/tabix.cpp
--../vcflib/tabixpp/bgzf.o: ../vcflib/tabixpp/bgzf.c ../vcflib/tabixpp/bgzf.h
+-../vcflib/tabixpp/tabix.o:
+- cd $(TABIX_ROOT)/ && make
+-../vcflib/tabixpp/htslib/bgzf.o: ../vcflib/tabixpp/htslib/bgzf.c ../vcflib/tabixpp/htslib/htslib/bgzf.h
- cd ../vcflib/tabixpp && $(MAKE)
-
-../vcflib/smithwaterman/SmithWatermanGotoh.o: ../vcflib/smithwaterman/SmithWatermanGotoh.h ../vcflib/smithwaterman/SmithWatermanGotoh.cpp
@@ -52,11 +53,13 @@ Description: vcflib needs to be packaged separately
VERSION_FILE=./version_git.h
RELEASED_VERSION_FILE=./version_release.txt
-@@ -257,5 +236,4 @@ autoversion:
+@@ -269,6 +246,5 @@ autoversion:
+
clean:
- rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a}
+- rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a}
- cd ../vcflib/smithwaterman && make clean
++ rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles
--- a/Makefile
+++ b/Makefile
@@ -66,227 +69,3 @@ Description: vcflib needs to be packaged separately
cd src && $(MAKE)
log: src/version_git.h
---- a/src/AlleleParser.cpp
-+++ b/src/AlleleParser.cpp
-@@ -485,7 +485,7 @@ void AlleleParser::setupVCFInput(void) {
- // variant input for analysis and targeting
- if (!parameters.variantPriorsFile.empty()) {
- variantCallInputFile.open(parameters.variantPriorsFile);
-- currentVariant = new vcf::Variant(variantCallInputFile);
-+ currentVariant = new vcflib::Variant(variantCallInputFile);
- usingVariantInputAlleles = true;
-
- // get sample names from VCF input file
-@@ -1108,7 +1108,7 @@ void AlleleParser::updateHaplotypeBasisA
- pos + referenceLength + CACHED_BASIS_HAPLOTYPE_WINDOW + 1)) {
- //cerr << "the vcf line " << haplotypeVariantInputFile.line << endl;
- // get the variants in the target region
-- vcf::Variant var(haplotypeVariantInputFile);
-+ vcflib::Variant var(haplotypeVariantInputFile);
- while (haplotypeVariantInputFile.getNextVariant(var)) {
- //cerr << "input variant: " << var << endl;
-
-@@ -1122,9 +1122,9 @@ void AlleleParser::updateHaplotypeBasisA
- }
- */
-
-- map<string, vector<vcf::VariantAllele> > variants = var.parsedAlternates();
-- for (map<string, vector<vcf::VariantAllele> >::iterator a = variants.begin(); a != variants.end(); ++a) {
-- for (vector<vcf::VariantAllele>::iterator v = a->second.begin(); v != a->second.end(); ++v) {
-+ map<string, vector<vcflib::VariantAllele> > variants = var.parsedAlternates();
-+ for (map<string, vector<vcflib::VariantAllele> >::iterator a = variants.begin(); a != variants.end(); ++a) {
-+ for (vector<vcflib::VariantAllele>::iterator v = a->second.begin(); v != a->second.end(); ++v) {
- //cerr << v->ref << "/" << v->alt << endl;
- if (v->ref != v->alt) {
- //cerr << "basis allele " << v->position << " " << v->ref << "/" << v->alt << endl;
-@@ -2107,7 +2107,7 @@ void AlleleParser::getInputVariantsInReg
- if (!usingVariantInputAlleles) return;
-
- // get the variants in the target region
-- vcf::Variant var(variantCallInputFile);
-+ vcflib::Variant var(variantCallInputFile);
- if (!seq.empty()) {
- variantCallInputFile.setRegion(seq, start, end);
- }
-@@ -2117,10 +2117,10 @@ void AlleleParser::getInputVariantsInReg
- long int pos = currentVariant->position - 1;
- // get alternate alleles
- bool includePreviousBaseForIndels = true;
-- map<string, vector<vcf::VariantAllele> > variantAlleles = currentVariant->parsedAlternates();
-+ map<string, vector<vcflib::VariantAllele> > variantAlleles = currentVariant->parsedAlternates();
- // TODO this would be a nice option: why does it not work?
-- //map<string, vector<vcf::VariantAllele> > variantAlleles = currentVariant->flatAlternates();
-- vector< vector<vcf::VariantAllele> > orderedVariantAlleles;
-+ //map<string, vector<vcflib::VariantAllele> > variantAlleles = currentVariant->flatAlternates();
-+ vector< vector<vcflib::VariantAllele> > orderedVariantAlleles;
- for (vector<string>::iterator a = currentVariant->alt.begin(); a != currentVariant->alt.end(); ++a) {
- orderedVariantAlleles.push_back(variantAlleles[*a]);
- }
-@@ -2128,14 +2128,14 @@ void AlleleParser::getInputVariantsInReg
- vector<Allele> genotypeAlleles;
- set<long int> alternatePositions;
-
-- for (vector< vector<vcf::VariantAllele> >::iterator g = orderedVariantAlleles.begin(); g != orderedVariantAlleles.end(); ++g) {
-+ for (vector< vector<vcflib::VariantAllele> >::iterator g = orderedVariantAlleles.begin(); g != orderedVariantAlleles.end(); ++g) {
-
-- vector<vcf::VariantAllele>& altAllele = *g;
-+ vector<vcflib::VariantAllele>& altAllele = *g;
-
- vector<Allele> alleles;
-
-- for (vector<vcf::VariantAllele>::iterator v = altAllele.begin(); v != altAllele.end(); ++v) {
-- vcf::VariantAllele& variant = *v;
-+ for (vector<vcflib::VariantAllele>::iterator v = altAllele.begin(); v != altAllele.end(); ++v) {
-+ vcflib::VariantAllele& variant = *v;
- long int allelePos = variant.position - 1;
- AlleleType type;
- string alleleSequence = variant.alt;
-@@ -2240,7 +2240,7 @@ void AlleleParser::updateInputVariants(l
- if (gotRegion) {
-
- // get the variants in the target region
-- vcf::Variant var(variantCallInputFile);
-+ vcflib::Variant var(variantCallInputFile);
- bool ok;
- while (ok = variantCallInputFile.getNextVariant(*currentVariant)) {
-
-@@ -2248,10 +2248,10 @@ void AlleleParser::updateInputVariants(l
- long int pos = currentVariant->position - 1;
- // get alternate alleles
- bool includePreviousBaseForIndels = true;
-- map<string, vector<vcf::VariantAllele> > variantAlleles = currentVariant->parsedAlternates();
-+ map<string, vector<vcflib::VariantAllele> > variantAlleles = currentVariant->parsedAlternates();
- // TODO this would be a nice option: why does it not work?
-- //map<string, vector<vcf::VariantAllele> > variantAlleles = currentVariant->flatAlternates();
-- vector< vector<vcf::VariantAllele> > orderedVariantAlleles;
-+ //map<string, vector<vcflib::VariantAllele> > variantAlleles = currentVariant->flatAlternates();
-+ vector< vector<vcflib::VariantAllele> > orderedVariantAlleles;
- for (vector<string>::iterator a = currentVariant->alt.begin(); a != currentVariant->alt.end(); ++a) {
- orderedVariantAlleles.push_back(variantAlleles[*a]);
- }
-@@ -2259,14 +2259,14 @@ void AlleleParser::updateInputVariants(l
- vector<Allele> genotypeAlleles;
- set<long int> alternatePositions;
-
-- for (vector< vector<vcf::VariantAllele> >::iterator g = orderedVariantAlleles.begin(); g != orderedVariantAlleles.end(); ++g) {
-+ for (vector< vector<vcflib::VariantAllele> >::iterator g = orderedVariantAlleles.begin(); g != orderedVariantAlleles.end(); ++g) {
-
-- vector<vcf::VariantAllele>& altAllele = *g;
-+ vector<vcflib::VariantAllele>& altAllele = *g;
-
- vector<Allele> alleles;
-
-- for (vector<vcf::VariantAllele>::iterator v = altAllele.begin(); v != altAllele.end(); ++v) {
-- vcf::VariantAllele& variant = *v;
-+ for (vector<vcflib::VariantAllele>::iterator v = altAllele.begin(); v != altAllele.end(); ++v) {
-+ vcflib::VariantAllele& variant = *v;
- long int allelePos = variant.position - 1;
- AlleleType type;
- string alleleSequence = variant.alt;
---- a/src/AlleleParser.h
-+++ b/src/AlleleParser.h
-@@ -163,9 +163,9 @@ public:
- BedReader bedReader;
-
- // VCF
-- vcf::VariantCallFile variantCallFile;
-- vcf::VariantCallFile variantCallInputFile; // input variant alleles, to target analysis
-- vcf::VariantCallFile haplotypeVariantInputFile; // input alleles which will be used to construct haplotype alleles
-+ vcflib::VariantCallFile variantCallFile;
-+ vcflib::VariantCallFile variantCallInputFile; // input variant alleles, to target analysis
-+ vcflib::VariantCallFile haplotypeVariantInputFile; // input alleles which will be used to construct haplotype alleles
-
- // input haplotype alleles
- //
-@@ -349,7 +349,7 @@ private:
-
- int currentRefID;
- BamAlignment currentAlignment;
-- vcf::Variant* currentVariant;
-+ vcflib::Variant* currentVariant;
-
- };
-
---- a/src/ResultData.cpp
-+++ b/src/ResultData.cpp
-@@ -5,8 +5,8 @@ using namespace std;
-
-
-
--vcf::Variant& Results::vcf(
-- vcf::Variant& var, // variant to update
-+vcflib::Variant& Results::vcf(
-+ vcflib::Variant& var, // variant to update
- BigFloat pHom,
- long double bestComboOddsRatio,
- //long double alleleSamplingProb,
-@@ -630,8 +630,8 @@ vcf::Variant& Results::vcf(
- }
-
-
--vcf::Variant& Results::gvcf(
-- vcf::Variant& var,
-+vcflib::Variant& Results::gvcf(
-+ vcflib::Variant& var,
- NonCalls& nonCalls,
- AlleleParser* parser) {
-
---- a/src/ResultData.h
-+++ b/src/ResultData.h
-@@ -41,8 +41,8 @@ public:
- }
- }
-
-- vcf::Variant& vcf(
-- vcf::Variant& var, // variant to update
-+ vcflib::Variant& vcf(
-+ vcflib::Variant& var, // variant to update
- BigFloat pHom,
- long double bestComboOddsRatio,
- //long double alleleSamplingProb,
-@@ -61,8 +61,8 @@ public:
- vector<string>& sequencingTechnologies,
- AlleleParser* parser);
-
-- vcf::Variant& gvcf(
-- vcf::Variant& var,
-+ vcflib::Variant& gvcf(
-+ vcflib::Variant& var,
- NonCalls& noncalls,
- AlleleParser* parser);
- };
---- a/src/freebayes.cpp
-+++ b/src/freebayes.cpp
-@@ -144,7 +144,7 @@ int main (int argc, char *argv[]) {
- || (parameters.gVCFchunk &&
- nonCalls.lastPos().second - nonCalls.firstPos().second
- > parameters.gVCFchunk))) {
-- vcf::Variant var(parser->variantCallFile);
-+ vcflib::Variant var(parser->variantCallFile);
- out << results.gvcf(var, nonCalls, parser) << endl;
- nonCalls.clear();
- }
-@@ -658,12 +658,12 @@ int main (int argc, char *argv[]) {
-
- // write the last gVCF record(s)
- if (parameters.gVCFout && !nonCalls.empty()) {
-- vcf::Variant var(parser->variantCallFile);
-+ vcflib::Variant var(parser->variantCallFile);
- out << results.gvcf(var, nonCalls, parser) << endl;
- nonCalls.clear();
- }
-
-- vcf::Variant var(parser->variantCallFile);
-+ vcflib::Variant var(parser->variantCallFile);
-
- out << results.vcf(
- var,
-@@ -696,7 +696,7 @@ int main (int argc, char *argv[]) {
- // write the last gVCF record
- if (parameters.gVCFout && !nonCalls.empty()) {
- Results results;
-- vcf::Variant var(parser->variantCallFile);
-+ vcflib::Variant var(parser->variantCallFile);
- out << results.gvcf(var, nonCalls, parser) << endl;
- nonCalls.clear();
- }
diff --git a/debian/patches/vcffirstheader.patch b/debian/patches/vcffirstheader.patch
new file mode 100644
index 0000000..070fcd0
--- /dev/null
+++ b/debian/patches/vcffirstheader.patch
@@ -0,0 +1,29 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 10 Feb 2017 09:09:35 +0100
+Description: This script was not part of the vcflib release
+ tarball but is available in Git
+ https://github.com/vcflib/vcflib/blob/master/scripts/vcffirstheader
+ Since it is used in the test suite of freebayes 1.1 it is installed
+ here as quilt patch. Once vcflib might be release including the
+ scripts directory the patch can be dropped and replaced by an according
+ symlink inside rules or by setting PATH accordingly
+
+--- /dev/null
++++ b/vcflib/scripts/vcffirstheader
+@@ -0,0 +1,16 @@
++#!/usr/bin/env python
++
++import sys
++
++header=True
++for line in sys.stdin:
++ if line.startswith('##'):
++ if header:
++ print line.strip()
++ continue
++ elif line.startswith('#'):
++ if header:
++ print line.strip()
++ header=False
++ continue
++ print line.strip()
diff --git a/debian/rules b/debian/rules
index 8045fdf..666b949 100755
--- a/debian/rules
+++ b/debian/rules
@@ -9,5 +9,9 @@ override_dh_auto_install:
override_dh_auto_test:
mkdir -p $(CURDIR)/test/bash-tap/
for bt in $(CURDIR)/debian/bash-tap/* ; do ln -s $${bt} $(CURDIR)/test/bash-tap/`basename $${bt}` ; done
- export PATH=/usr/lib/vcflib/binaries/:$(PATH) dh_auto_test && echo "Tests were running successfully"
+ ln -s $(CURDIR)/debian/test-simple-bash/lib test/test-simple-bash
+ chmod +x vcflib/scripts/vcffirstheader
+ # export PATH=/usr/lib/vcflib/binaries/:$(PATH) dh_auto_test
+ echo "Tests should be run" && PATH=/usr/lib/vcflib/binaries/:$(PATH) dh_auto_test && echo "Tests were running successfully"
rm -rf $(CURDIR)/test/bash-tap
+ rm test/test-simple-bash/lib
diff --git a/debian/test-simple-bash/lib/test-simple.bash b/debian/test-simple-bash/lib/test-simple.bash
new file mode 100644
index 0000000..dab44e7
--- /dev/null
+++ b/debian/test-simple-bash/lib/test-simple.bash
@@ -0,0 +1,110 @@
+# test-simple.bash - Simple TAP test framework for Bash
+#
+# Copyright (c) 2013 Ingy döt Net
+
+TestSimple_VERSION='0.0.1'
+
+TestSimple.init() {
+ TestSimple_plan=0
+ TestSimple_run=0
+ TestSimple_failed=0
+ TestSimple_usage='Usage: source test-simple.bash tests <number>'
+
+ if [ $# -gt 0 ]; then
+ [[ $# -eq 2 ]] && [[ "$1" == 'tests' ]] ||
+ TestSimple.die "$TestSimple_usage"
+ [[ "$2" =~ ^-?[0-9]+$ ]] ||
+ TestSimple.die 'Plan must be a number'
+ [[ $2 -gt 0 ]] ||
+ TestSimple.die 'Plan must greater then 0'
+ TestSimple_plan=$2
+ printf "1..%d\n" $TestSimple_plan
+ fi
+
+ trap TestSimple.END EXIT
+}
+
+ok() {
+ local args=("$@")
+ local last=$((${#args[@]} - 1))
+ local label=''
+ local ending_re='^]]?$'
+ let TestSimple_run=TestSimple_run+1
+ (
+ set +e
+ local rc=
+ if [[ $last -gt 0 ]] && [[ ! "${args[$last]}" =~ $ending_re ]]; then
+ label="${args[$last]}"
+ unset args[$last]
+ fi
+ if [[ ${#args[@]} -eq 1 ]] && [[ "${args[0]}" =~ ^[0-9]+$ ]]; then
+ rc=${args[0]}
+ elif [ ${args[0]} == '[[' ]; then
+ # XXX Currently need eval to support [[. Is there another way?
+ # Is [[ overkill? So many questons!
+ eval "${args[@]}" &> /dev/null
+ rc=$?
+ else
+ "${args[@]}" &> /dev/null
+ rc=$?
+ fi
+ if [ $rc -eq 0 ]; then
+ if [ -n "$label" ]; then
+ echo "ok $TestSimple_run - $label"
+ else
+ echo "ok $TestSimple_run"
+ fi
+ else
+ let TestSimple_failed=TestSimple_failed+1
+ if [ -n "$label" ]; then
+ echo "not ok $TestSimple_run - $label"
+ TestSimple.failure "$label"
+ else
+ echo "not ok $TestSimple_run"
+ TestSimple.failure "$label"
+ fi
+ fi
+ return $rc
+ )
+}
+
+TestSimple_CALL_STACK_LEVEL=1
+TestSimple.failure() {
+ local c=( $(caller $TestSimple_CALL_STACK_LEVEL) )
+ local file=${c[2]}
+ local line=${c[0]}
+ local label="$1"
+ label=${label:+"'$label'\n# at $file line $line."}
+ label=${label:-"at $file line $line."}
+ echo -e "# Failed test $label" >&2
+}
+
+TestSimple.END() {
+ for v in plan run failed; do eval local $v=\$TestSimple_$v; done
+ if [ $plan -eq 0 ]; then
+ if [ $run -gt 0 ]; then
+ echo "# Tests were run but no plan was declared." >&2
+ fi
+ else
+ if [ $run -eq 0 ]; then
+ echo "# No tests run!" >&2
+ elif [ $run -ne $plan ]; then
+ local msg="# Looks like you planned $plan tests but ran $run."
+ [ $plan -eq 1 ] && msg=${msg/tests/test}
+ echo "$msg" >&2
+ fi
+ fi
+ local exit_code=0
+ if [ $TestSimple_failed -gt 0 ]; then
+ exit_code=$TestSimple_failed
+ [ $exit_code -gt 254 ] && exit_code=254
+ local msg="# Looks like you failed $failed tests of $run run."
+ [ $TestSimple_failed -eq 1 ] && msg=${msg/tests/test}
+ echo "$msg" >&2
+ fi
+ exit $exit_code
+}
+
+TestSimple.die() { echo "$@" >&2; trap EXIT; exit 255; }
+
+[[ "${BASH_SOURCE[0]}" != "${0}" ]] && TestSimple.init "$@"
diff --git a/debian/test-simple-bash/test/basics.t b/debian/test-simple-bash/test/basics.t
new file mode 100644
index 0000000..61949ea
--- /dev/null
+++ b/debian/test-simple-bash/test/basics.t
@@ -0,0 +1,26 @@
+#!/bin/bash
+
+PATH=lib:$PATH
+source test-simple.bash tests 14
+
+ok 0 '0 is true'
+ok $((6 * 7 -42)) 'Math result is 0'
+ok true 'true is ok'
+ok $(false || true; echo $?) 'Expression expansion'
+
+ls &> /dev/null
+ok $? '$? is success'
+ls --qqq &> /dev/null
+ok $((! $?)) 'Negate $? failure'
+
+fruit=apple
+
+ok [ $fruit = apple ] '[ … ] testing works'
+ok [ "0" == "0" -a 1 -eq 1 ] '[ … -a … ] (AND) testing works'
+ok [ ${fruit/a/A} = Apple ] 'Substitution expansion works'
+ok [ "${fruit}s" = 'app''les' ] 'Quote removal works'
+ok [[ $fruit = apple ]] '[[ … ]] works'
+ok [[ $fruit == apple ]] '== works'
+ok [[ $((6 * 7)) -eq 42 ]] '-eq works with math expression'
+ok $(ls | grep lib &> /dev/null; echo $?) \
+ 'Testing a grep command works'
diff --git a/debian/test-simple-bash/test/doc.t b/debian/test-simple-bash/test/doc.t
new file mode 100644
index 0000000..7d77db7
--- /dev/null
+++ b/debian/test-simple-bash/test/doc.t
@@ -0,0 +1,15 @@
+#!/bin/bash
+
+question() { echo yes; }
+
+PATH=lib:$PATH
+source test-simple.bash tests 5
+
+ok 0 '0 is true (other numbers are false)'
+
+answer=$(question "...?")
+ok [ $answer == yes ] 'The answer is yes!'
+ok [[ $answer =~ ^y ]] 'The answer begins with y'
+
+ok true 'true is ok'
+ok '! false' '! false is true'
diff --git a/debian/test-simple-bash/test/no-label.t b/debian/test-simple-bash/test/no-label.t
new file mode 100644
index 0000000..9b58eb4
--- /dev/null
+++ b/debian/test-simple-bash/test/no-label.t
@@ -0,0 +1,25 @@
+#!/bin/bash
+
+PATH=lib:$PATH
+source test-simple.bash tests 14
+
+ok 0
+ok $((6 * 7 -42))
+ok true
+ok $(false || true; echo $?)
+
+ls &> /dev/null
+ok $?
+ls --qqq &> /dev/null
+ok $((! $?))
+
+fruit=apple
+
+ok [ $fruit = apple ]
+ok [ "0" == "0" -a 1 -eq 1 ]
+ok [ ${fruit/a/A} = Apple ]
+ok [ "${fruit}s" = 'app''les' ]
+ok [[ $fruit = apple ]]
+ok [[ $fruit == apple ]]
+ok [[ $((6 * 7)) -eq 42 ]]
+ok $(ls | grep lib &> /dev/null; echo $?)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/freebayes.git
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