Commit c1be661e authored by Steffen Möller's avatar Steffen Möller
Browse files

New upstream version 2.29.2+dfsg

parent f08fe72c

.github/workflows/main.yml

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name: CI



on: [push, pull_request]



jobs:

  build:



    runs-on: ubuntu-latest



    steps:

    - uses: actions/checkout@v1

    - name: Install samtools

      run: sudo apt-get install -y samtools 

    - name: Compile and test Bedtools

      run: make -j8 && make test

    - name: Compile static binary

      run:  make -j8 static

    - uses: actions/upload-artifact@v1

      with:

          name: bedtools.static

          path: bin/bedtools.static

.travis.yml

deleted100644 → 0
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os:

  - osx

  - linux

language: cpp

compiler:

  - gcc

  - clang

addons:

  apt:

    packages:

    - samtools

    - tabix

script: make test

Makefile

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@@ -16,6 +16,7 @@ CCPREFIX = 
else

CCPREFIX = @

endif



OBJ_DIR	= obj

BIN_DIR	= bin

SRC_DIR	= src
@@ -131,6 +132,8 @@ ALL_LIBS = $(BT_LIBS) $(LIBS) 


all: print_banner $(BIN_DIR)/bedtools $(BIN_DIR)/intersectBed



static: print_banner $(BIN_DIR)/bedtools.static



BUILT_OBJECTS = $(OBJ_DIR)/bedtools.o

# Include all the Makefile fragments, which add to $(BUILT_OBJECTS)

include $(patsubst %,%/Makefile.frag,$(SUBDIRS) $(UTIL_SUBDIRS))
@@ -148,7 +151,7 @@ DEPFLAGS = -MT $@ -MMD -MP -MF $*.Td 


define CXX_COMPILE

@echo "  * compiling $<"

$(CCPREFIX)$(CXX) $(ALL_CXXFLAGS) $(ALL_CPPFLAGS) $(DEPFLAGS) -c -o $@ $<

$(CCPREFIX) $(CC_WRAPPER) $(CXX) $(ALL_CXXFLAGS) $(ALL_CPPFLAGS) $(DEPFLAGS) -c -o $@ $<

@mv -f $*.Td $*.d

endef
@@ -170,7 +173,12 @@ $(BUILT_OBJECTS): | $(OBJ_DIR) 


$(BIN_DIR)/bedtools: autoversion $(BUILT_OBJECTS) $(HTSDIR)/libhts.a | $(BIN_DIR)

	@echo "- Building main bedtools binary."

	$(CCPREFIX)$(CXX) $(ALL_LDFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) $(HTSDIR)/libhts.a $(ALL_LIBS)

	$(CCPREFIX) $(CC_WRAPPER) $(CXX) $(ALL_LDFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) $(HTSDIR)/libhts.a $(ALL_LIBS)

	@echo "done."



$(BIN_DIR)/bedtools.static: autoversion $(BUILT_OBJECTS) $(HTSDIR)/libhts.a | $(BIN_DIR)

	@echo "- Building main bedtools binary."

	$(CCPREFIX) $(CC_WRAPPER) $(CXX) -static $(ALL_LDFLAGS) -o $(BIN_DIR)/bedtools.static $(BUILT_OBJECTS) $(HTSDIR)/libhts.a $(ALL_LIBS)

	@echo "done."



$(BIN_DIR)/intersectBed: | $(BIN_DIR)

docs/conf.py

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@@ -44,16 +44,16 @@ master_doc = 'index' 


# General information about the project.

project = u'bedtools'

copyright = u'2009 - 2017, Aaron R. Quinlan and Neil Kindlon'

copyright = u'2009 - 2019, Aaron R. Quinlan and Neil Kindlon'



# The version info for the project you're documenting, acts as replacement for

# |version| and |release|, also used in various other places throughout the

# built documents.

#

# The short X.Y version.

version = '2.29.0'

version = '2.29.1'

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

release = '2.29.0'

release = '2.29.1'



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

# for a list of supported languages.

docs/content/history.rst

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@@ -2,6 +2,18 @@ 
Release History

###############



Version 2.29.1 (9-Dec-2019)

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

1. Fixed a `bug <https://github.com/arq5x/bedtools2/issues/773>`_ that now allows blocked intersection to be counted based on unique base pairs of overlap. The resolution for `issue 750 <https://github.com/arq5x/bedtools2/issues/750>`_ in version 2.29.0 mistakenly allowed for fractional overlap to be counted based upon redundant overlap. 

2. Moved to Github Continuous Integration for automatic testing.

3. Fixed a `bug <https://github.com/arq5x/bedtools2/issues/799>`_ that injected erroneous quality values with BAM records had no valid quality values.

4. Fixed a `bug <https://github.com/arq5x/bedtools2/issues/609>`_ that destroyed backwards compatibility in the `getfasta` tool. Thanks to Torsten Seeman for reporting this.

5. Fixed a corner case `bug <https://github.com/arq5x/bedtools2/issues/711>`_ in the `reldist` tool.

6. Fixed a `bug <https://github.com/arq5x/bedtools2/issues/788>`_ in the `bedtobam` tool that caused the last character in read names to be removed.

7. Fixed a `bug <https://github.com/arq5x/bedtools2/issues/779>`_ causing a segfault in the `jaccard` tool.

8. Fixed a `bug <https://github.com/arq5x/bedtools2/issues/777>`_ causing a corner case issue in the way coordinates are reported in the `flank` tool.





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.