Steffen Möller · Steffen Möller · Steffen Möller · Steffen Möller · Steffen Möller · Steffen Möller
--- a/.gitignore
+++ b/.gitignore
@@ -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
--- a/.travis.yml
+++ b/.travis.yml
+os:
+  - osx
+  - linux
 language: cpp
 compiler:
  - gcc

--- a/Makefile
+++ b/Makefile
@@ -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

--- a/debian/changelog
+++ b/debian/changelog
+bedtools (2.28.0+dfsg-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream version
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0
+
+  * Semi-automated update with Andreas' routine-update script,
+    only reintroduced the conflicts of the test package with earlier
+    releases of bedtools.
+
+ -- Steffen Moeller <moeller@debian.org>  Fri, 26 Jul 2019 17:33:35 +0200
+
 bedtools (2.27.1+dfsg-4) unstable; urgency=medium

  * Disable the shuffle test on other 32-bit architectures.

--- a/debian/compat
+++ b/debian/compat
-11
--- a/debian/control
+++ b/debian/control
@@ -4,11 +4,11 @@ Uploaders: Charles Plessy <plessy@debian.org>,
           Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
               python,
               zlib1g-dev,
               samtools
-Standards-Version: 4.3.0
+Standards-Version: 4.4.0
 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

--- a/debian/patches/fix_test_script.patch
+++ b/debian/patches/fix_test_script.patch
@@ -2,8 +2,10 @@ Author: Andreas Tille <tille@debian.org>
 Last-Update: Tue, 14 Jul 2015 11:01:25 +0200
 Description: Use environment variable to find bedtools in all cases

--- a/test/merge/test-merge.sh
-+++ b/test/merge/test-merge.sh
+Index: bedtools/test/merge/test-merge.sh
+===================================================================
+--- bedtools.orig/test/merge/test-merge.sh
+++ bedtools/test/merge/test-merge.sh
 @@ -467,7 +467,7 @@ chr1	30	100	.,.,.
 chr2	10	20	.
 chr2	30	40	.

--- a/debian/patches/flag_no_overwrite
+++ b/debian/patches/flag_no_overwrite
 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
-@@ -18,9 +18,9 @@
+@@ -22,9 +22,9 @@ 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 += -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)
+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 += -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
+-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 @@
+@@ -42,7 +42,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
-+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
+-	$(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 @@
+@@ -38,7 +38,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
-+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
+-	$(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 @@
+@@ -40,7 +40,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
-+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
+-	$(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 @@
+@@ -30,7 +30,7 @@ BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
-+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+-	$(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 @@
+@@ -85,7 +85,7 @@ all: $(BUILT_OBJECTS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
-+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
+-	$(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."
--- a/debian/patches/gzstream.h.patch
+++ b/debian/patches/gzstream.h.patch
 Description: To find gzstream.h during Debian package building.
 Author: Charles Plessy <plessy@debian.org>
 Forwarded: no
--- a/src/utils/gzstream/gzstream.C
-+++ b/src/utils/gzstream/gzstream.C
+Index: bedtools/src/utils/gzstream/gzstream.C
+===================================================================
+--- bedtools.orig/src/utils/gzstream/gzstream.C
+++ bedtools/src/utils/gzstream/gzstream.C
 @@ -26,7 +26,7 @@
 // Standard C++ Library".
 // ============================================================================

--- a/debian/patches/remove_barski_binding_site.png.patch
+++ b/debian/patches/remove_barski_binding_site.png.patch
@@ -2,8 +2,10 @@ Author: Andreas Tille <tille@debian.org>
 Last-Update: Mon, 18 Jul 2016 16:13:29 +0200
 Desctiption: Delete reference to removed file

--- a/docs/content/tools/genomecov.rst
-+++ b/docs/content/tools/genomecov.rst
+Index: bedtools/docs/content/tools/genomecov.rst
+===================================================================
+--- bedtools.orig/docs/content/tools/genomecov.rst
+++ bedtools/docs/content/tools/genomecov.rst
 @@ -346,11 +346,8 @@ overlaps to be performed.
 Coverage by fragment
 ==============================================================================

--- a/debian/patches/reproducible_build.patch
+++ b/debian/patches/reproducible_build.patch
@@ -3,14 +3,16 @@ Last-Update: Fri, 12 Aug 2016 00:22:02 +0100
 Bug-Debian: https://bugs.debian.org/834110
 Description: Enable reproducible builds

--- a/Makefile
-+++ b/Makefile
-@@ -107,7 +107,7 @@ UTIL_SUBDIRS =	$(SRC_DIR)/utils/FileReco
- 				$(SRC_DIR)/utils/ToolBase \
- 				$(SRC_DIR)/utils/driver
+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)
 
 
- INCLUDES =	-I$(SRC_DIR)/utils/bedFile \
+ REAL_SRC_DIR=$(shell pwd)/$(SRC_DIR)
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -2,5 +2,7 @@ gzstream.h.patch
 fix_test_script.patch
 remove_barski_binding_site.png.patch
 reproducible_build.patch
-louder
+# louder was apparently already performed by upstream
+#louder
+# not Debian-specific, upstream has worked on that, too
 flag_no_overwrite
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -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.

--- a/docs/content/faq.rst
+++ b/docs/content/faq.rst
@@ -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


--- a/docs/content/history.rst
+++ b/docs/content/history.rst
@@ -2,6 +2,13 @@
 Release History
 ###############

+Version 2.28.0 (23-Mar-2019)
+============================
+1. Included support for htslib to enable CRAM support and long-term stability (Thanks to Hao Hou!)
+2. Included support for genomes with large chromosomes by moving to 64-bit integeres throughout the code base. Thanks to Brent Pedersen and John Marshall!
+3. We now provide a statically-linked binary for LINUX (not OSX) systems.
+4. Various minor bug fixes.
+
 Version 2.27.0 (6-Dec-2017)
 ============================
 1. Fixed a big memory leak and algorithmic flaw in the `split` option. Thanks to Neil Kindlon!

--- a/docs/content/installation.rst
+++ b/docs/content/installation.rst
@@ -16,6 +16,17 @@ release from package managers such as
 Installing stable releases
 --------------------------

+.....................................
+Downloading a pre-compiled binary
+.....................................
+.. note::    
+    1. The following approach will only work for Linux (non-OSX) systems.
+
+Starting with release 2.28.0, wqe provide statically-linked binaries thast should work
+right away on Linux systems. Go to the `releases <https://github.com/arq5x/bedtools2/releases>`_
+page and look for the static binary named `bedtools`. Right click on it, get the URL, then download it
+with `wget` or `curl` and you should be good to go.
+
 .....................................
 Compiling from source via Github
 .....................................
@@ -26,16 +37,13 @@ the `releases <https://github.com/arq5x/bedtools2/releases>`_ tab.
 The following commands will install ``bedtools`` in a local directory on an UNIX or OS X machine.

 .. note::    
-    1. This example is based on version 2.25.0. For future releasese, you should replace 
-    the version number with the version you intend to install.
-    
-    2. The bedtools Makefiles utilize the GCC compiler. One should edit the
+    1. The bedtools Makefiles utilize the GCC compiler. One should edit the
    Makefiles accordingly if one wants to use a different compiler.

 .. code-block:: bash

-  $ wget https://github.com/arq5x/bedtools2/releases/download/v2.25.0/bedtools-2.25.0.tar.gz 
-  $ tar -zxvf bedtools-2.25.0.tar.gz
+  $ wget https://github.com/arq5x/bedtools2/releases/download/v2.28.0/bedtools-2.28.0.tar.gz 
+  $ tar -zxvf bedtools-2.28.0.tar.gz
  $ cd bedtools2
  $ make


--- a/docs/content/overview.rst
+++ b/docs/content/overview.rst
@@ -281,7 +281,7 @@ Assaf.
 ----------------------------------------------------------------------------
 Support for “split” or “spliced” BAM alignments and “blocked” BED features
 ----------------------------------------------------------------------------
-As of Version 2.8.0, five bedtools (``intersect``, ``coverage``, ``genomecob``,
+As of Version 2.8.0, five bedtools (``intersect``, ``coverage``, ``genomecov``,
 ``bamToBed``, and ``bed12ToBed6``) can properly handle “split”/”spliced” BAM alignments (i.e., having an
 “N” CIGAR operation) and/or “blocked” BED (aka BED12) features.


--- a/docs/content/related-tools.rst
+++ b/docs/content/related-tools.rst
@@ -70,7 +70,7 @@ Source code can be obtained on `GitHub <https://github.com/tk2/RetroSeq>`_.
 Intersphinx documentation
 -------------------------
 BEDTools documentation pages are available via Intersphinx (http://sphinx-doc.org/ext/intersphinx.html).
-To enable this, add the following to conf.py in a Sphinx proejct:
+To enable this, add the following to conf.py in a Sphinx project:

    intersphinx_mapping = {'bedtools': ('http://bedtools.readthedocs.org/en/latest/', None)}
    

--- a/docs/content/tools/bamtobed.rst
+++ b/docs/content/tools/bamtobed.rst
@@ -43,7 +43,7 @@ Option          Description
                to BED12. `Forces -split`.
 **-split**      Report each portion of a "split" BAM (i.e., having an "N" CIGAR 
                operation) alignment as a distinct BED intervals.
-**-splitD**     Report each portion of a "split" BAM while obeying noth "N" CIGAR 
+**-splitD**     Report each portion of a "split" BAM while obeying both "N" CIGAR 
                and "D" operation. Forces `-split`.
 **-ed**         Use the "edit distance" tag (NM) for the BED score field. 
                Default for BED is to use mapping quality. Default for BEDPE is 

--- a/docs/content/tools/bamtofastq.rst
+++ b/docs/content/tools/bamtofastq.rst
@@ -6,6 +6,15 @@
 ``bedtools bamtofastq`` is a conversion utility for extracting FASTQ records
 from sequence alignments in BAM format. 

+
+.. note::
+
+    If you are using CRAM as input, you will need to specify
+    the *full path* describing the location of the relevant reference genome in FASTA format via the CRAM_REFERENCE environment variable. For example:
+
+        `export CRAM_REFERENCE=/path/to/ref/g1k_v37_decoy.fa`
+
+
 ==========================================================================
 Usage and option summary
 ==========================================================================