Merge branch 'master' into codacy-badge

.gitignore

@@ -5,3 +5,4 @@ bin/
 pypairix.egg-info/
 dist/
 build/
+samples/1_2_merged11.bsorted.pairs.gz*

.travis.yml

@@ -1,8 +1,23 @@
-language: c python 
-sudo: true
+language: c python
+sudo: required
 compiler: gcc
-script: 
- - make
- - python setup.py install
- - python test/test.py
- - source test/test_c.sh
+python:
+- '3.6'
+- '2.7'
+env:
+- VALGRIND_TEST_ON=1
+before_install:
+- sudo apt-get install -qq valgrind
+script:
+- make
+- |
+  if [[ $TRAVIS_PYTHON_VERSION == 3.6 ]]; then
+  sudo python3 setup.py install
+  python3 test/test.py
+  fi
+- |
+  if [[ $TRAVIS_PYTHON_VERSION == 2.7 ]]; then
+  sudo python setup.py install
+  python test/test.py
+  fi
+- source test/test_c.sh  # valgrind test is applied when VALGRIND_TEST_ON=1

MANIFEST.in

@@ -1,2 +1,3 @@
 include src/*.h
 include LICENSE.txt
+include VERSION.txt

Makefile

@@ -1,70 +1,2 @@
-CC=			gcc
-CFLAGS=		-g -Wall -O2 -fPIC #-m64 #-arch ppc
-DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -DBGZF_CACHE
-LOBJS=		bgzf.o kstring.o knetfile.o index.o bedidx.o
-AOBJS=		main.o
-PROG=		pairix bgzip pairs_merger streamer_1d 
-INCLUDES=
-SUBDIRS=	.
-LIBPATH=
-LIBCURSES=
-
-.SUFFIXES:.c .o
-
-.c.o:
-		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
-
-all-recur lib-recur clean-recur cleanlocal-recur install-recur:
-		@target=`echo $@ | sed s/-recur//`; \
-		wdir=`pwd`; \
-		list='$(SUBDIRS)'; for subdir in $$list; do \
-			cd $$subdir; \
-			$(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
-				INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
-			cd $$wdir; \
-		done;
-
-all:$(PROG)
-		mkdir -p bin; mv pairix bgzip pairs_merger streamer_1d bin; chmod +x bin/*
-
-lib:libpairix.a
-
-libpairix.so.1:$(LOBJS)
-		$(CC) -shared -Wl,-soname,libpairix.so -o $@ $(LOBJS) -lc -lz
-
-libpairix.1.dylib:$(LOBJS)
-		libtool -dynamic $(LOBJS) -o $@ -lc -lz
-
-libpairix.a:$(LOBJS)
-		$(AR) -csru $@ $(LOBJS)
-
-pairix:lib $(AOBJS)
-		$(CC) $(CFLAGS) -o $@ $(AOBJS) -L. -lpairix -lm $(LIBPATH) -lz
-
-bgzip:bgzip.o bgzf.o knetfile.o
-		$(CC) $(CFLAGS) -o $@ bgzip.o bgzf.o knetfile.o -lz
-
-pairs_merger:pairs_merger.o lib
-		$(CC) $(CFLAGS) -o $@ pairs_merger.o -L. -lpairix -lm $(LIBPATH) -lz
-
-streamer_1d:streamer_1d.o lib
-		$(CC) $(CFLAGS) -o $@ streamer_1d.o -L. -lpairix -lm $(LIBPATH) -lz
-
-TabixReader.class:TabixReader.java
-		javac -cp .:sam.jar TabixReader.java
-
-kstring.o:kstring.h
-knetfile.o:knetfile.h
-bgzf.o:bgzf.h knetfile.h
-index.o:bgzf.h pairix.h khash.h ksort.h kstring.h
-main.o:pairix.h kstring.h bgzf.h
-pairs_merger.o:pairix.h kstring.h bgzf.h
-streamer_1d.o:pairix.h kstring.h bgzf.h
-bgzip.o:bgzf.h
-bedidx.o:kseq.h khash.h
-
-
-cleanlocal:
-		rm -fr gmon.out *.o a.out *.dSYM $(PROG) *~ *.a tabix.aux tabix.log *.class libpairix.*.dylib libpairix.so*
-
-clean:cleanlocal-recur
+all:
+	cd src; make; cd ..

README.md

@@ -96,6 +96,7 @@ make
 # In order to use utils, add util path to PATH
 # In order to use bam2pairs, add util/bam2pairs to PATH
 # eg: PATH=~/git/pairix/bin/:~/git/pairix/util:~/git/pairix/util/bam2pairs:$PATH
+
 ```
 Alternatively, `conda install pairix` can be used to install both Pairix and Pypairix together. This requires Anaconda or Miniconda.
 <br>
@@ -111,6 +112,8 @@ sudo yum install zlib-devel
 
 <br>
 
+<br>
+
 ### Usage for pairix
 #### Compression
 ```

VERSION.txt

@@ -0,0 +1 @@
+0.3.3