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......@@ -22,10 +22,8 @@ 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/*/exp
test/*/obs
test/genomecov/pair-chip.bam
test/bigchroms/bigx.fasta
test/bigchroms/bigx.fasta.fai
LICENSE
View file @ ded652c7
GNU GENERAL PUBLIC LICENSE
Version 2, June 1991
Copyright (C) 1989, 1991 Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
Preamble
The licenses for most software are designed to take away your
freedom to share and change it. By contrast, the GNU General Public
License is intended to guarantee your freedom to share and change free
software--to make sure the software is free for all its users. This
General Public License applies to most of the Free Software
Foundation's software and to any other program whose authors commit to
using it. (Some other Free Software Foundation software is covered by
the GNU Lesser General Public License instead.) You can apply it to
your programs, too.
When we speak of free software, we are referring to freedom, not
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To protect your rights, we need to make restrictions that forbid
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We protect your rights with two steps: (1) copyright the software, and
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The precise terms and conditions for copying, distribution and
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GNU GENERAL PUBLIC LICENSE
TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
0. This License applies to any program or other work which contains
a notice placed by the copyright holder saying it may be distributed
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Whether that is true depends on what the Program does.
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These requirements apply to the modified work as a whole. If
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FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
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END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest
to attach them to the start of each source file to most effectively
convey the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.
<one line to give the program's name and a brief idea of what it does.>
Copyright (C) <year> <name of author>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
Also add information on how to contact you by electronic and paper mail.
If the program is interactive, make it output a short notice like this
when it starts in an interactive mode:
Gnomovision version 69, Copyright (C) year name of author
Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License. Of course, the commands you use may
be called something other than `show w' and `show c'; they could even be
mouse-clicks or menu items--whatever suits your program.
You should also get your employer (if you work as a programmer) or your
school, if any, to sign a "copyright disclaimer" for the program, if
necessary. Here is a sample; alter the names:
Yoyodyne, Inc., hereby disclaims all copyright interest in the program
`Gnomovision' (which makes passes at compilers) written by James Hacker.
<signature of Ty Coon>, 1 April 1989
Ty Coon, President of Vice
This General Public License does not permit incorporating your program into
proprietary programs. If your program is a subroutine library, you may
consider it more useful to permit linking proprietary applications with the
library. If this is what you want to do, use the GNU Lesser General
Public License instead of this License.
The MIT License
Copyright (c) 2009-2019 Aaron Quinlan
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:
The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE
Makefile
View file @ ded652c7
......@@ -12,30 +12,33 @@ RELEASED_VERSION_FILE=./src/utils/version/version_release.txt
# define our object and binary directories
ifeq ($(VERBOSE),1)
export CCPREFIX =
CCPREFIX =
else
export CCPREFIX = @
CCPREFIX = @
endif
export OBJ_DIR = obj
export BIN_DIR = bin
export SRC_DIR = src
export UTIL_DIR = src/utils
export CXX = g++
OBJ_DIR = obj
BIN_DIR = bin
SRC_DIR = src
CXX = g++
ifeq ($(DEBUG),1)
export CXXFLAGS = -Wconversion -Wall -Wextra -DDEBUG -D_DEBUG -g -O0 -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES)
BT_CPPFLAGS = -DDEBUG -D_DEBUG -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES)
BT_CXXFLAGS = -Wconversion -Wall -Wextra -g -O0
else
export CXXFLAGS = -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES)
BT_CPPFLAGS = -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES)
BT_CXXFLAGS = -g -Wall -O2
endif
# If the user has specified to do so, tell the compile to use rand() (instead of mt19937).
ifeq ($(USE_RAND),1)
export CXXFLAGS += -DUSE_RAND
BT_CXXFLAGS += -DUSE_RAND
else
export CXXFLAGS += -std=c++11
BT_CXXFLAGS += -std=c++11
endif
export LIBS = -lz -lm -lbz2 -llzma -lpthread
export BT_ROOT = src/utils/BamTools/
BT_LDFLAGS =
BT_LIBS = -lz -lm -lbz2 -llzma -lpthread
prefix ?= /usr/local
......@@ -79,6 +82,7 @@ SUBDIRS = $(SRC_DIR)/annotateBed \
$(SRC_DIR)/spacingFile \
$(SRC_DIR)/split \
$(SRC_DIR)/subtractFile \
$(SRC_DIR)/summaryFile \
$(SRC_DIR)/tagBam \
$(SRC_DIR)/unionBedGraphs \
$(SRC_DIR)/windowBed \
......@@ -108,61 +112,68 @@ 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/htslib
BUILT_OBJECTS = $(OBJ_DIR)/*.o
REAL_SRC_DIR=$(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."
$(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."
$(SRC_DIR)/utils/driver
@echo "- Creating executables for old CLI."
@python scripts/makeBashScripts.py
@chmod +x bin/*
@echo "done."
INCLUDES = $(addprefix -I,$(SUBDIRS) $(UTIL_SUBDIRS)) \
-I$(SRC_DIR)/utils/BamTools/include \
-I$(HTSDIR) \
-I$(SRC_DIR)/utils/lineFileUtilities \
-I$(SRC_DIR)/utils/Point \
-I$(SRC_DIR)/utils/stringUtilities
# Ensure that the user's $CXXFLAGS/etc are applied after bedtools's.
ALL_CXXFLAGS = $(BT_CXXFLAGS) $(CXXFLAGS)
ALL_CPPFLAGS = $(BT_CPPFLAGS) $(CPPFLAGS)
ALL_LDFLAGS = $(BT_LDFLAGS) $(LDFLAGS)
ALL_LIBS = $(BT_LIBS) $(LIBS)
all: print_banner $(BIN_DIR)/bedtools $(BIN_DIR)/intersectBed
all-static: print_banner $(OBJ_DIR) $(BIN_DIR) autoversion $(UTIL_SUBDIRS) $(SUBDIRS)
BUILT_OBJECTS = $(OBJ_DIR)/bedtools.o
# Include all the Makefile fragments, which add to $(BUILT_OBJECTS)
include $(patsubst %,%/Makefile.frag,$(SUBDIRS) $(UTIL_SUBDIRS))
## Automatically generate C++ dependencies.
## $(DEPFLAGS) is a set of compiler flags that causes the compiler to generate
## dependencies as a byproduct (which we write to a temporary file, only moving
## it into place on successful compilations).
## We then include the dependency files into this Makefile.
## The subdirectories' Makefile fragments contain rules like the one for
## $(OBJ_DIR)/bedtools.o below, with a dependency on obj/foo.d so that if
## the dependency file is missing the target will be rebuilt.
##
DEPFLAGS = -MT $@ -MMD -MP -MF $*.Td
define CXX_COMPILE
@echo " * compiling $<"
$(CCPREFIX)$(CXX) $(ALL_CXXFLAGS) $(ALL_CPPFLAGS) $(DEPFLAGS) -c -o $@ $<
@mv -f $*.Td $*.d
endef
$(OBJ_DIR)/%.d: ;
.PRECIOUS: $(OBJ_DIR)/%.d
-include $(patsubst %.o,%.d,$(BUILT_OBJECTS))
$(OBJ_DIR)/bedtools.o: $(SRC_DIR)/bedtools.cpp $(OBJ_DIR)/bedtools.d
$(CXX_COMPILE)
# HTSlib's htslib.mk provides rules to rebuild $(HTSDIR)/libhts.a.
HTSDIR = src/utils/htslib
include $(HTSDIR)/htslib.mk
# This order-only prerequisite ensures OBJ_DIR exists before building any .o file
# but ignores the directory's timestamp, which changes every time a .o file is written.
$(BUILT_OBJECTS): | $(OBJ_DIR)
$(BIN_DIR)/bedtools: autoversion $(BUILT_OBJECTS) $(HTSDIR)/libhts.a | $(BIN_DIR)
@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)
$(CCPREFIX)$(CXX) $(ALL_LDFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) $(HTSDIR)/libhts.a $(ALL_LIBS)
@echo "done."
$(BIN_DIR)/intersectBed: | $(BIN_DIR)
@echo "- Creating executables for old CLI."
@python scripts/makeBashScripts.py
@chmod +x bin/*
......@@ -180,7 +191,7 @@ install: all
print_banner:
@echo "Building BEDTools:"
@echo "========================================================="
$(info $$CXXFLAGS is [${CXXFLAGS}])
@echo "CXXFLAGS is [$(ALL_CXXFLAGS)]"
.PHONY: print_banner
# make the "obj/" and "bin/" directories, if they don't exist
......@@ -188,18 +199,13 @@ $(OBJ_DIR) $(BIN_DIR):
@mkdir -p $@
# 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.
.PHONY: $(UTIL_SUBDIRS) $(SUBDIRS)
$(UTIL_SUBDIRS) $(SUBDIRS): $(OBJ_DIR) $(BIN_DIR)
@echo "- Building in $@"
@$(MAKE) --no-print-directory --directory=$@
# Usually HTSlib's configure script has not been used (detected via config.mk
# not existing), so clean should also remove the generated config.h.
clean:
@echo " * Cleaning up."
@rm -f $(VERSION_FILE) $(OBJ_DIR)/* $(BIN_DIR)/*
@cd src/utils/htslib && make clean > /dev/null
@test -e src/utils/htslib/config.mk || rm -f src/utils/htslib/config.h
.PHONY: clean
test: all
......
README.md
View file @ ded652c7
......@@ -33,12 +33,12 @@ Details
First created through urgency and adrenaline by Aaron Quinlan Spring 2009.
Maintained by the Quinlan Laboratory at the University of Virginia.
1. **Lead developers**: Aaron Quinlan, Neil Kindlon
1. **Lead developers**: Aaron Quinlan, Hao Hoou, Brent Pedersen, Neil Kindlon
2. **Significant contributions**: Assaf Gordon, Royden Clark, John Marshall, Brent Pedersen, Ryan Dale
3. **Repository**: https://github.com/arq5x/bedtools2
4. **Stable releases**: https://github.com/arq5x/bedtools2/releases
5. **Documentation**: http://bedtools.readthedocs.org
6. **License**: Released under GNU public license version 2 (GPL v2).
6. **License**: Released under MIT license
Citation
......
RELEASE_HISTORY deleted 100644 → 0
View file @ 53bc2d95
This diff is collapsed.
debian/changelog
View file @ ded652c7
bedtools (2.29.0+dfsg-1) unstable; urgency=medium
* Team upload.
* New upstream version
* Removed Chris' reproducible builds patch - upstream diverged too much
-- Steffen Moeller <moeller@debian.org> Tue, 05 Nov 2019 21:41:22 +0100
bedtools (2.28.0+dfsg1-1) unstable; urgency=medium
* Use 2to3 to port to Python3
......
debian/control
View file @ ded652c7
......@@ -10,7 +10,7 @@ Build-Depends: debhelper-compat (= 12),
libbz2-dev,
liblzma-dev,
samtools
Standards-Version: 4.4.0
Standards-Version: 4.4.1
Vcs-Browser: https://salsa.debian.org/med-team/bedtools
Vcs-Git: https://salsa.debian.org/med-team/bedtools.git
Homepage: https://github.com/arq5x/bedtools2
......@@ -36,8 +36,6 @@ Architecture: all
Multi-Arch: foreign
Depends: ${misc:Depends}
Suggests: bedtools
Breaks: bedtools (<< 2.19.1-1)
Replaces: bedtools (<< 2.19.1-1)
Description: test data for the bedtools package
Test data for the BEDTools suite of utilities for comparing genomic features.
It is distributed in a separate package because it is large and
......
debian/patches/flag_no_overwrite deleted 100644 → 0
View file @ 53bc2d95
From: Michael R. Crusoe <michael.crusoe@gmail.com>
Subject: Don't overwrite CXXFLAGS & include missing CPPFLAGS as needed
Index: bedtools/Makefile
===================================================================
--- bedtools.orig/Makefile
+++ bedtools/Makefile
@@ -22,9 +22,9 @@ export SRC_DIR = src
export UTIL_DIR = src/utils
export CXX = g++
ifeq ($(DEBUG),1)
-export CXXFLAGS = -Wconversion -Wall -Wextra -DDEBUG -D_DEBUG -g -O0 -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES)
+export CXXFLAGS += -Wconversion -Wall -Wextra -DDEBUG -D_DEBUG -g -O0 -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES)
else
-export CXXFLAGS = -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(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).
Index: bedtools/src/complementFile/Makefile
===================================================================
--- bedtools.orig/src/complementFile/Makefile
+++ bedtools/src/complementFile/Makefile
@@ -42,7 +42,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
- $(CCPREFIX) $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
+ $(CCPREFIX) $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
Index: bedtools/src/coverageFile/Makefile
===================================================================
--- bedtools.orig/src/coverageFile/Makefile
+++ bedtools/src/coverageFile/Makefile
@@ -38,7 +38,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
- $(CCPREFIX) $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
+ $(CCPREFIX) $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
Index: bedtools/src/subtractFile/Makefile
===================================================================
--- bedtools.orig/src/subtractFile/Makefile
+++ bedtools/src/subtractFile/Makefile
@@ -40,7 +40,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
- $(CCPREFIX) $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
+ $(CCPREFIX) $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
Index: bedtools/src/utils/ToolBase/Makefile
===================================================================
--- bedtools.orig/src/utils/ToolBase/Makefile
+++ bedtools/src/utils/ToolBase/Makefile
@@ -30,7 +30,7 @@ BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
- $(CCPREFIX) $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+ $(CCPREFIX) $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
$(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(INCLUDES)
@@ -39,4 +39,4 @@ clean:
@echo "Cleaning up."
@rm -f $(OBJ_DIR)/ToolBase.o
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
Index: bedtools/src/utils/driver/Makefile
===================================================================
--- bedtools.orig/src/utils/driver/Makefile
+++ bedtools/src/utils/driver/Makefile
@@ -85,7 +85,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
- $(CCPREFIX) $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
+ $(CCPREFIX) $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
debian/patches/reproducible_build.patch
View file @ ded652c7
......@@ -3,16 +3,3 @@ Last-Update: Fri, 12 Aug 2016 00:22:02 +0100
Bug-Debian: https://bugs.debian.org/834110
Description: Enable reproducible builds
Index: bedtools/Makefile
===================================================================
--- bedtools.orig/Makefile
+++ bedtools/Makefile
@@ -111,7 +111,7 @@ UTIL_SUBDIRS = $(SRC_DIR)/utils/FileReco
$(SRC_DIR)/utils/driver \
$(SRC_DIR)/utils/htslib
-BUILT_OBJECTS = $(OBJ_DIR)/*.o
+BUILT_OBJECTS = $(sort $(OBJ_DIR)/*.o)
REAL_SRC_DIR=$(shell pwd)/$(SRC_DIR)
debian/patches/series
View file @ ded652c7
gzstream.h.patch
fix_test_script.patch
remove_barski_binding_site.png.patch
reproducible_build.patch
# louder was apparently already performed by upstream
#louder
# not Debian-specific, upstream has worked on that, too
flag_no_overwrite
#flag_no_overwrite
2to3.patch
debian/rules
View file @ ded652c7
......@@ -12,8 +12,9 @@ endif
%:
dh $@
override_dh_installchangelogs:
dh_installchangelogs RELEASE_HISTORY
# File no longer exists
#override_dh_installchangelogs:
# dh_installchangelogs RELEASE_HISTORY
override_dh_install:
dh_install
......
docs/conf.py
View file @ ded652c7
......@@ -51,9 +51,9 @@ copyright = u'2009 - 2017, Aaron R. Quinlan and Neil Kindlon'
# built documents.
#
# The short X.Y version.
version = '2.28.0'
version = '2.29.0'
# The full version, including alpha/beta/rc tags.
release = '2.28.0'
release = '2.29.0'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
......
docs/content/history.rst
View file @ ded652c7
......@@ -2,6 +2,20 @@
Release History
###############
Version 2.29.0 (3-Sep-2019)
============================
1. Added a new `-C` option to the `intersect` tool that separately reports the count of intersections observed for each database (`-b`) file given. Formerly, the `-c` option reported to sum of all intersections observed across all database files.
2. Fixed an important `bug <https://github.com/arq5x/bedtools2/issues/750>`_ in `intersect` that prevented some split reads from being counted properly with using the `-split` option with the `-f` option.
3. Fixed a bug in `shuffle` such that shuffled regions should have the same strand as the chose `-incl` region.
4. Added a new `-L` option to `L`imit the output of the `complement` tool to solely the chromosomes that are represented in the `-i` file.
5. Fixed a regression in the `multicov` tool introduced in 2.28 that caused incorrect counts.
6. Added support for multi-mapping reads in the `bamtofastq` tool.
7. Fixed a `bug <https://github.com/arq5x/bedtools2/issues/301>`_ that prevented the "window" tool from properly adding interval "slop" to BAM records.
8. Fixed a `bug <https://github.com/arq5x/bedtools2/issues/195>`_ that caused the `slop` tool to not truncate an interval's end coordinate when it overlapped the end of a chromosome.
9. Added support for the "=" and "X" CIGAR operations to `bamtobed`.
10. Various other minor bug fixes and improvements to documentation.
Version 2.28.0 (23-Mar-2019)
============================
1. Included support for htslib to enable CRAM support and long-term stability (Thanks to Hao Hou!)
......
docs/content/overview.rst
View file @ ded652c7
......@@ -35,49 +35,53 @@ Summary of available tools.
bedtools support a wide range of operations for interrogating and manipulating genomic features. The table below summarizes
the tools available in the suite.
=========================== =========================================================================================================================================================
=============================================== ========================================================================
Utility Description
=========================== =========================================================================================================================================================
**annotate** Annotate coverage of features from multiple files.
**bamtobed** Convert BAM alignments to BED (& other) formats.
**bamtofastq** Convert BAM records to FASTQ records.
**bed12tobed6** Breaks BED12 intervals into discrete BED6 intervals.
**bedpetobam** Convert BEDPE intervals to BAM records.
**bedtobam** Convert intervals to BAM records.
**closest** Find the closest, potentially non-overlapping interval.
**cluster** Cluster (but don't merge) overlapping/nearby intervals.
**complement** Extract intervals _not_ represented by an interval file.
**coverage** Compute the coverage over defined intervals.
**expand** Replicate lines based on lists of values in columns.
**flank** Create new intervals from the flanks of existing intervals.
**genomecov** Compute the coverage over an entire genome.
**getfasta** Use intervals to extract sequences from a FASTA file.
**groupby** Group by common cols. & summarize oth. cols. (~ SQL "groupBy")
**igv** Create an IGV snapshot batch script.
**intersect** Find overlapping intervals in various ways.
**jaccard** Calculate the Jaccard statistic b/w two sets of intervals.
**links** Create a HTML page of links to UCSC locations.
**makewindows** Make interval "windows" across a genome.
**map** Apply a function to a column for each overlapping interval.
**maskfasta** Use intervals to mask sequences from a FASTA file.
**merge** Combine overlapping/nearby intervals into a single interval.
**multicov** Counts coverage from multiple BAMs at specific intervals.
**multiinter** Identifies common intervals among multiple interval files.
**nuc** Profile the nucleotide content of intervals in a FASTA file.
**overlap** Computes the amount of overlap from two intervals.
**pairtobed** Find pairs that overlap intervals in various ways.
**pairtopair** Find pairs that overlap other pairs in various ways.
**random** Generate random intervals in a genome.
**reldist** Calculate the distribution of relative distances b/w two files.
**shift** Adjust the position of intervals.
**shuffle** Randomly redistribute intervals in a genome.
**slop** Adjust the size of intervals.
**sort** Order the intervals in a file.
**subtract** Remove intervals based on overlaps b/w two files.
**tag** Tag BAM alignments based on overlaps with interval files.
**unionbedg** Combines coverage intervals from multiple BEDGRAPH files.
**window** Find overlapping intervals within a window around an interval.
=========================== =========================================================================================================================================================
=============================================== ========================================================================
:doc:`tools/annotate` Annotate coverage of features from multiple files.
:doc:`tools/bamtobed` Convert BAM alignments to BED (& other) formats.
:doc:`tools/bamtofastq` Convert BAM records to FASTQ records.
:doc:`tools/bed12tobed6` Breaks BED12 intervals into discrete BED6 intervals.
:doc:`tools/bedpetobam` Convert BEDPE intervals to BAM records.
:doc:`tools/bedtobam` Convert intervals to BAM records.
:doc:`tools/closest` Find the closest, potentially non-overlapping interval.
:doc:`tools/cluster` Cluster (but don't merge) overlapping/nearby intervals.
:doc:`tools/complement` Extract intervals _not_ represented by an interval file.
:doc:`tools/coverage` Compute the coverage over defined intervals.
:doc:`tools/expand` Replicate lines based on lists of values in columns.
:doc:`tools/fisher` Calculate Fisher statistic b/w two feature files.
:doc:`tools/flank` Create new intervals from the flanks of existing intervals.
:doc:`tools/genomecov` Compute the coverage over an entire genome.
:doc:`tools/getfasta` Use intervals to extract sequences from a FASTA file.
:doc:`tools/groupby` Group by common cols. & summarize oth. cols. (~ SQL "groupBy")
:doc:`tools/igv` Create an IGV snapshot batch script.
:doc:`tools/intersect` Find overlapping intervals in various ways.
:doc:`tools/jaccard` Calculate the Jaccard statistic b/w two sets of intervals.
:doc:`tools/links` Create a HTML page of links to UCSC locations.
:doc:`tools/makewindows` Make interval "windows" across a genome.
:doc:`tools/map` Apply a function to a column for each overlapping interval.
:doc:`tools/maskfasta` Use intervals to mask sequences from a FASTA file.
:doc:`tools/merge` Combine overlapping/nearby intervals into a single interval.
:doc:`tools/multicov` Counts coverage from multiple BAMs at specific intervals.
:doc:`tools/multiinter` Identifies common intervals among multiple interval files.
:doc:`tools/nuc` Profile the nucleotide content of intervals in a FASTA file.
:doc:`tools/overlap` Computes the amount of overlap from two intervals.
:doc:`tools/pairtobed` Find pairs that overlap intervals in various ways.
:doc:`tools/pairtopair` Find pairs that overlap other pairs in various ways.
:doc:`tools/random` Generate random intervals in a genome.
:doc:`tools/reldist` Calculate the distribution of relative distances b/w two files.
:doc:`tools/sample` Sample random records from file using reservoir sampling.
:doc:`tools/shift` Adjust the position of intervals.
:doc:`tools/shuffle` Randomly redistribute intervals in a genome.
:doc:`tools/slop` Adjust the size of intervals.
:doc:`tools/sort` Order the intervals in a file.
:doc:`tools/spacing` Sample random records from file using reservoir sampling.
:doc:`tools/split` Split a file into multiple files with equal records or base pairs.
:doc:`tools/subtract` Remove intervals based on overlaps b/w two files.
:doc:`tools/tag` Tag BAM alignments based on overlaps with interval files.
:doc:`tools/unionbedg` Combines coverage intervals from multiple BEDGRAPH files.
:doc:`tools/window` Find overlapping intervals within a window around an interval.
=============================================== ========================================================================
......
docs/content/tools/complement.rst
View file @ ded652c7
......@@ -58,5 +58,29 @@ covered by at least one record from the input file.
chr1 800 1000
chr2 0 800
==========================================================================
``-L`` Only report chromosomes that are in the `-i` file
==========================================================================
Use the "**-L**" option to `L`imit the output to solely the chromosomes
that are represented in the `-i` file. Chromosomes that are in `-g` but
not `-i` will be suppressed
For example (note the difference in coverage with and without **-s**:
.. code-block:: bash
$ cat A.bed
chr1 100 200
chr1 400 500
chr1 500 800
$ cat my.genome
chr1 1000
chr2 800
$ bedtools complement -i A.bed -g my.genome
chr1 0 100
chr1 200 400
chr1 800 1000
docs/content/tools/intersect.rst
View file @ ded652c7
......@@ -73,7 +73,8 @@ Option Description
**-wo** Write the original A and B entries plus the number of base pairs of overlap between the two features. Only A features with overlap are reported. Restricted by -f and -r.
**-wao** Write the original A and B entries plus the number of base pairs of overlap between the two features. However, A features w/o overlap are also reported with a NULL B feature and overlap = 0. Restricted by -f and -r.
**-u** Write original A entry once if any overlaps found in B. In other words, just report the fact at least one overlap was found in B. Restricted by -f and -r.
**-c** For each entry in A, report the number of hits in B while restricting to -f. Reports 0 for A entries that have no overlap with B. Restricted by -f and -r.
**-c** For each entry in A, report the number of hits in B while restricting to -f. Reports 0 for A entries that have no overlap with B. Restricted -f, -F, -r, and -s.
**-C** For each entry in A, separately report the number of overlaps with each B file on a distinct line. Reports 0 for A entries that have no overlap with B. Overlaps restricted by -f, -F, -r, and -s.
**-v** Only report those entries in A that have no overlap in B. Restricted by -f and -r.
**-f** Minimum overlap required as a fraction of A. Default is 1E-9 (i.e. 1bp).
**-F** Minimum overlap required as a fraction of B. Default is 1E-9 (i.e., 1bp).
......@@ -502,8 +503,68 @@ features found in "B". Therefore, *each feature in A is reported once*.
chr1 10 20 2
chr1 30 40 0
The `-c` option can also work with multiple -B files. In this case, the reported count will reflect the total number of intersections observed across _all_ `-B` files. It will not report a separate count for each database file. This can be achieved with the `-C` option.
.. code-block:: bash
$ cat A.bed
chr1 10 20
chr1 30 40
$ cat B.bed
chr1 15 20
chr1 18 25
$ cat C.bed
chr1 16 21
chr1 19 26
$ bedtools intersect -a A.bed -b B.bed -c
chr1 10 20 4
chr1 30 40 0
==========================================================================
``-C`` Reporting the number of overlapping features for each database file
==========================================================================
Unlike the the `-c` option, in the case of multiple `-B` files, the `-C` option will report a separate count for each database file.
.. code-block:: bash
$ cat A.bed
chr1 10 20
chr1 30 40
$ cat B.bed
chr1 15 20
chr1 18 25
$ cat C.bed
chr1 16 21
chr1 19 26
$ bedtools intersect -a A.bed -b B.bed -C
chr1 10 20 1 2
chr1 10 20 2 2
chr1 30 40 1 0
chr1 30 40 1 0
If you would like to see more useful information than the file _number_ from which the counts came, one can use the `-filenames` or `-names` options.
.. code-block:: bash
$ bedtools intersect -a A.bed -b B.bed -C -filenames
chr1 10 20 A.bed 2
chr1 10 20 B.bed 2
chr1 30 40 A.bed 0
chr1 30 40 B.bed 0
$ bedtools intersect -a A.bed -b B.bed -C -names a b
chr1 10 20 a 2
chr1 10 20 b 2
chr1 30 40 a 0
chr1 30 40 b 0
=======================================================================
``-v`` Reporting the absence of any overlapping features
......
docs/content/tools/subtract.rst
View file @ ded652c7
......@@ -11,10 +11,7 @@
|
``bedtools subtract`` searches for features in B that overlap A. If an
overlapping feature is found in B, the overlapping portion is removed from A
and the remaining portion of A is reported. If a feature in B overlaps all of a
feature in A, the A feature will not be reported.
``bedtools subtract`` bedtools` subtract searches for features in B that overlap A by at least the number of base pairs given by the -f option. If an overlapping feature is found in B, the overlapping portion is removed from A and the remaining portion of A is reported. If a feature in B overlaps all of a feature in A, the A feature will not be reported. If a feature in B does not overlap a feature in A by at least the -f amount, the A feature will be reported in its entirety.
===============================
......
src/annotateBed/Makefile deleted 100644 → 0
View file @ 53bc2d95
UTILITIES_DIR = ../utils/
OBJ_DIR = ../../obj/
BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
-I$(UTILITIES_DIR)/lineFileUtilities/ \
-I$(UTILITIES_DIR)/BamTools/ \
-I$(UTILITIES_DIR)/gzstream/ \
-I$(UTILITIES_DIR)/fileType/ \
-I$(UTILITIES_DIR)/version/
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= annotateMain.cpp annotateBed.cpp annotateBed.h
OBJECTS= annotateMain.o annotateBed.o
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
all: $(BUILT_OBJECTS)
.PHONY: all
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
$(CCPREFIX) $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
@rm -f $(OBJ_DIR)/annotateMain.o $(OBJ_DIR)/annotateBed.o
.PHONY: clean
src/annotateBed/Makefile.frag 0 → 100644
View file @ ded652c7
BUILT_OBJECTS += obj/annotateMain.o obj/annotateBed.o
obj/annotateMain.o: src/annotateBed/annotateMain.cpp obj/annotateMain.d
$(CXX_COMPILE)
obj/annotateBed.o: src/annotateBed/annotateBed.cpp obj/annotateBed.d
$(CXX_COMPILE)
src/bamToBed/Makefile deleted 100644 → 0
View file @ 53bc2d95
UTILITIES_DIR = ../utils/
OBJ_DIR = ../../obj/
BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
-I$(UTILITIES_DIR)/gzstream/ \
-I$(UTILITIES_DIR)/lineFileUtilities/ \
-I$(UTILITIES_DIR)/fileType/ \
-I$(UTILITIES_DIR)/BamTools/include \
-I$(UTILITIES_DIR)/BlockedIntervals \
-I$(UTILITIES_DIR)/version/
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= bamToBed.cpp
OBJECTS= bamToBed.o
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
all: $(BUILT_OBJECTS)
.PHONY: all
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
$(CCPREFIX) $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
@rm -f $(OBJ_DIR)/bamToBed.o
.PHONY: clean