Commit 45adb388 authored by Steffen Möller's avatar Steffen Möller
Browse files

New upstream version 2.28.0+dfsg

parent c6cc5501

.gitignore

+17 −0
Original line number Diff line number Diff line
@@ -12,3 +12,20 @@ src/utils/version/version_git.h 
.cproject

nbproject

sandbox

test/general/o

test/genomecov/chip.bam

test/genomecov/one_block.bam

test/genomecov/pair-chip.bam

test/genomecov/sam-w-del.bam

test/genomecov/three_blocks.bam

test/multicov/one_block.bam.bai

test/multicov/two_blocks.bam.bai

test/genomecov/two_blocks.bam

test/shift/genome.len

test/split/exp



src/utils/htslib/test/test-bcf-translate

src/utils/htslib/test/test_realn

test/genomecov/pair-chip.bam

test/bigchroms/bigx.fasta

test/bigchroms/bigx.fasta.fai

.travis.yml

+3 −0
Original line number Diff line number Diff line 
os:

  - osx

  - linux

language: cpp

compiler:

  - gcc

Makefile

+54 −44
Original line number Diff line number Diff line
@@ -10,17 +10,21 @@ VERSION_FILE=./src/utils/version/version_git.h 
RELEASED_VERSION_FILE=./src/utils/version/version_release.txt







# define our object and binary directories

ifeq ($(VERBOSE),1)

export CCPREFIX = 

else

export CCPREFIX = @

endif

export OBJ_DIR	= obj

export BIN_DIR	= bin

export SRC_DIR	= src

export UTIL_DIR	= src/utils

export CXX		= g++

ifeq ($(DEBUG),1)

export CXXFLAGS = -Wall -Wextra -DDEBUG -D_DEBUG -g -O0 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)

export CXXFLAGS = -Wconversion -Wall -Wextra -DDEBUG -D_DEBUG -g -O0 -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES)

else

export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)

export CXXFLAGS = -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES)

endif



# If the user has specified to do so, tell the compile to use rand() (instead of mt19937).
@@ -30,7 +34,7 @@ else 
export CXXFLAGS += -std=c++11

endif 



export LIBS		= -lz

export LIBS		= -lz -lm -lbz2 -llzma -lpthread

export BT_ROOT  = src/utils/BamTools/



prefix ?= /usr/local
@@ -97,7 +101,6 @@ UTIL_SUBDIRS = $(SRC_DIR)/utils/FileRecordTools \ 
				$(SRC_DIR)/utils/NewChromsweep \

				$(SRC_DIR)/utils/sequenceUtilities \

				$(SRC_DIR)/utils/tabFile \

				$(SRC_DIR)/utils/BamTools \

				$(SRC_DIR)/utils/BamTools-Ancillary \

				$(SRC_DIR)/utils/BlockedIntervals \

				$(SRC_DIR)/utils/Fasta \
@@ -105,46 +108,59 @@ UTIL_SUBDIRS = $(SRC_DIR)/utils/FileRecordTools \ 
				$(SRC_DIR)/utils/GenomeFile \

				$(SRC_DIR)/utils/RecordOutputMgr \

				$(SRC_DIR)/utils/ToolBase \

				$(SRC_DIR)/utils/driver

				$(SRC_DIR)/utils/driver \

				$(SRC_DIR)/utils/htslib



BUILT_OBJECTS = $(OBJ_DIR)/*.o





INCLUDES =	-I$(SRC_DIR)/utils/bedFile \

				-I$(SRC_DIR)/utils/BinTree \

				-I$(SRC_DIR)/utils/version \

				-I$(SRC_DIR)/utils/bedGraphFile \

				-I$(SRC_DIR)/utils/chromsweep \

				-I$(SRC_DIR)/utils/Contexts \

				-I$(SRC_DIR)/utils/FileRecordTools \

				-I$(SRC_DIR)/utils/FileRecordTools/FileReaders \

				-I$(SRC_DIR)/utils/FileRecordTools/Records \

				-I$(SRC_DIR)/utils/general \

				-I$(SRC_DIR)/utils/gzstream \

				-I$(SRC_DIR)/utils/fileType \

				-I$(SRC_DIR)/utils/gzstream/ \

				-I$(SRC_DIR)/utils/lineFileUtilities \

				-I$(SRC_DIR)/utils/KeyListOps \

				-I$(SRC_DIR)/utils/NewChromsweep \

				-I$(SRC_DIR)/utils/sequenceUtilities \

				-I$(SRC_DIR)/utils/tabFile \

				-I$(SRC_DIR)/utils/BamTools \

				-I$(SRC_DIR)/utils/BamTools/include \

				-I$(SRC_DIR)/utils/BamTools/src \

				-I$(SRC_DIR)/utils/BamTools-Ancillary \

				-I$(SRC_DIR)/utils/BlockedIntervals \

				-I$(SRC_DIR)/utils/Fasta \

				-I$(SRC_DIR)/utils/VectorOps \

				-I$(SRC_DIR)/utils/GenomeFile \

				-I$(SRC_DIR)/utils/RecordOutputMgr \

				-I$(SRC_DIR)/utils/ToolBase \

				-I$(SRC_DIR)/utils/driver \

REAL_SRC_DIR=$(shell pwd)/$(SRC_DIR)



INCLUDES =	-I"$(REAL_SRC_DIR)/utils/bedFile" \

				-I"$(REAL_SRC_DIR)/utils/BinTree" \

				-I"$(REAL_SRC_DIR)/utils/version" \

				-I"$(REAL_SRC_DIR)/utils/bedGraphFile" \

				-I"$(REAL_SRC_DIR)/utils/chromsweep" \

				-I"$(REAL_SRC_DIR)/utils/Contexts" \

				-I"$(REAL_SRC_DIR)/utils/FileRecordTools" \

				-I"$(REAL_SRC_DIR)/utils/FileRecordTools/FileReaders" \

				-I"$(REAL_SRC_DIR)/utils/FileRecordTools/Records" \

				-I"$(REAL_SRC_DIR)/utils/general" \

				-I"$(REAL_SRC_DIR)/utils/gzstream" \

				-I"$(REAL_SRC_DIR)/utils/fileType" \

				-I"$(REAL_SRC_DIR)/utils/gzstream/" \

				-I"$(REAL_SRC_DIR)/utils/lineFileUtilities" \

				-I"$(REAL_SRC_DIR)/utils/KeyListOps" \

				-I"$(REAL_SRC_DIR)/utils/NewChromsweep" \

				-I"$(REAL_SRC_DIR)/utils/sequenceUtilities" \

				-I"$(REAL_SRC_DIR)/utils/tabFile" \

				-I"$(REAL_SRC_DIR)/utils/BamTools/include" \

				-I"$(REAL_SRC_DIR)/utils/BamTools-Ancillary" \

				-I"$(REAL_SRC_DIR)/utils/BlockedIntervals" \

				-I"$(REAL_SRC_DIR)/utils/Fasta" \

				-I"$(REAL_SRC_DIR)/utils/VectorOps" \

				-I"$(REAL_SRC_DIR)/utils/GenomeFile" \

				-I"$(REAL_SRC_DIR)/utils/RecordOutputMgr" \

				-I"$(REAL_SRC_DIR)/utils/ToolBase" \

				-I"$(REAL_SRC_DIR)/utils/driver" \

				-I"$(REAL_SRC_DIR)/utils/htslib"





all: print_banner $(OBJ_DIR) $(BIN_DIR) autoversion $(UTIL_SUBDIRS) $(SUBDIRS)

	@echo "- Building main bedtools binary."

	@$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES)

	@$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) $(LDFLAGS) $(INCLUDES)

	$(CCPREFIX) $(CXX) $(CXXFLAGS) $(CPPFLAGS) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES)

	$(CCPREFIX) $(CXX) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) $(SRC_DIR)/utils/htslib/libhts.a $(LIBS) $(LDFLAGS)

	@echo "done."



	@echo "- Creating executables for old CLI."

	@python scripts/makeBashScripts.py

	@chmod +x bin/*

	@echo "done."



all-static: print_banner $(OBJ_DIR) $(BIN_DIR) autoversion $(UTIL_SUBDIRS) $(SUBDIRS)

	@echo "- Building main bedtools binary."

	$(CCPREFIX) $(CXX) $(CXXFLAGS) $(CPPFLAGS) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES)

	$(CCPREFIX) $(CXX) -static -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) $(SRC_DIR)/utils/htslib/libhts.a $(LIBS) $(LDFLAGS)

	@echo "done."



	@echo "- Creating executables for old CLI."
@@ -172,12 +188,6 @@ $(OBJ_DIR) $(BIN_DIR): 
	@mkdir -p $@





# One special case: All (or almost all) programs requires the BamTools API files to be created first.

.PHONY: bamtools_api

bamtools_api:

	@$(MAKE) --no-print-directory --directory=$(BT_ROOT) api

$(UTIL_SUBDIRS) $(SUBDIRS): bamtools_api





# even though these are real directories, treat them as phony targets, forcing to always go in them are re-make.

# a future improvement would be the check for the compiled object, and rebuild only if the source code is newer.
@@ -187,9 +197,9 @@ $(UTIL_SUBDIRS) $(SUBDIRS): $(OBJ_DIR) $(BIN_DIR) 
	@$(MAKE) --no-print-directory --directory=$@



clean:

	@$(MAKE) --no-print-directory --directory=$(BT_ROOT) clean_api

	@echo " * Cleaning up."

	@rm -f $(VERSION_FILE) $(OBJ_DIR)/* $(BIN_DIR)/*

	@cd src/utils/htslib && make clean > /dev/null

.PHONY: clean



test: all

docs/conf.py

+3 −3
Original line number Diff line number Diff line
@@ -26,7 +26,7 @@ sys.path.append(os.path.abspath('pyplots')) 
# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.

extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 

              'sphinx.ext.intersphinx', 'sphinx.ext.todo', 

              'sphinx.ext.coverage', 'sphinx.ext.pngmath', 

              'sphinx.ext.coverage', 

              'sphinx.ext.ifconfig', 'sphinx.ext.viewcode',

			        'matplotlib.sphinxext.plot_directive']
@@ -51,9 +51,9 @@ copyright = u'2009 - 2017, Aaron R. Quinlan and Neil Kindlon' 
# built documents.

#

# The short X.Y version.

version = '2.27.0'

version = '2.28.0'

# The full version, including alpha/beta/rc tags.

release = '2.27.0'

release = '2.28.0'



# The language for content autogenerated by Sphinx. Refer to documentation

# for a list of supported languages.

docs/content/faq.rst

+1 −1
Original line number Diff line number Diff line
@@ -42,7 +42,7 @@ and on Fedora/Centos this would be: 
--------------------------------------------------

Compiling with a specific zlib library

--------------------------------------------------

If you need to override the location of the zlib lbrary used to compile bedtools, you can run `make` and specify the `LIBS` argument. For example:

If you need to override the location of the zlib library used to compile bedtools, you can run `make` and specify the `LIBS` argument. For example:



.. code-block:: bash