Merge branch 'master' into candidate-scoring-gpu

.travis.yml

@@ -1,11 +1,46 @@
 # travis.yml for github.com/jts/nanopolish
 
-language: cpp
+dist: trusty
+sudo: false
+language: generic
+cache: apt
+git:
+    depth: 1
+
+matrix:
+    include:
+    # Set env for both nanoplish and the dependency hdf5.
+    - env:
+        - CC=gcc-4.8
+        - CXX=g++-4.8
+        - AR=gcc-ar-4.8
+        - NM=gcc-nm-4.8
+        - RANLIB=gcc-ranlib-4.8
+    - env:
+        - CC=gcc-8
+        - CXX=g++-8
+        - AR=gcc-ar-8
+        - NM=gcc-nm-8
+        - RANLIB=gcc-ranlib-8
 
 # Install and export newer gcc
 before_install:
     - sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test
     - sudo apt-get update -qq
-    - sudo apt-get install -qq g++-4.8
+    - |
+      if [[ "${CC}" =~ ^gcc- ]]; then
+          echo "Installing ${CC}."
+          sudo apt-get install -qq "${CC}"
+      fi
+    - |
+      if [[ "${CXX}" =~ ^g\+\+- ]]; then
+          echo "Installing ${CXX}."
+          sudo apt-get install -qq "${CXX}"
+      fi
 
-script: make CXX=g++-4.8 nanopolish && make CXX=g++-4.8 test
+script:
+    # Suppress all compiler warnings for hdf5 Makefile
+    # to display the log without downloading the raw log on Travis log page.
+    # Travis finishs with error when exceeding the limit of 4 MB of log length.
+    - export H5_CFLAGS="-w"
+    - make nanopolish && make test

Makefile

@@ -8,8 +8,8 @@ SUBDIRS := src src/hmm src/thirdparty src/thirdparty/scrappie src/common src/ali
 #
 
 #Basic flags every build needs
-LIBS=-lz
-CXXFLAGS ?= -O3
+LIBS = -lz
+CXXFLAGS ?= -g -O3
 CXXFLAGS += -std=c++11 -fopenmp -fsigned-char
 CFLAGS ?= -std=c99 -O3
 CXX ?= g++
@@ -19,9 +19,9 @@ NVCCFLAGS ?= -std=c++11 -I. -I/usr/local/cuda-9.0include -O3 -use_fast_math --de
 CURTFLAGS ?= -L/usr/local/cuda-9.0/lib64 -lcudart
 
 # Change the value of HDF5, EIGEN, or HTS below to any value to disable compilation of bundled code
-HDF5?=install
-EIGEN?=install
-HTS?=install
+HDF5 ?= install
+EIGEN ?= install
+HTS ?= install
 
 # Check operating system, OSX doesn't have -lrt
 UNAME_S := $(shell uname -s)
@@ -31,53 +31,54 @@ endif
 
 # Default to automatically installing hdf5
 ifeq ($(HDF5), install)
-    H5_LIB=./lib/libhdf5.a
-    H5_INCLUDE=-I./include
+    H5_LIB = ./lib/libhdf5.a
+    H5_INCLUDE = -I./include
     LIBS += -ldl
 else
     # Use system-wide hdf5
-    H5_LIB=
-    H5_INCLUDE=
+    H5_LIB =
+    H5_INCLUDE =
     LIBS += -lhdf5
 endif
 
 # Default to automatically installing EIGEN
 ifeq ($(EIGEN), install)
-    EIGEN_CHECK=eigen/INSTALL
+    EIGEN_CHECK = eigen/INSTALL
 else
     # Use system-wide eigen
-    EIGEN_CHECK=
+    EIGEN_CHECK =
 endif
 
 # Default to build and link the libhts submodule
 ifeq ($(HTS), install)
-    HTS_LIB=./htslib/libhts.a
-    HTS_INCLUDE=-I./htslib
+    HTS_LIB = ./htslib/libhts.a
+    HTS_INCLUDE = -I./htslib
 else
     # Use system-wide htslib
-    HTS_LIB=
-    HTS_INCLUDE=
+    HTS_LIB =
+    HTS_INCLUDE =
     LIBS += -lhts
 endif
 
 # Include the header-only fast5 library
-FAST5_INCLUDE=-I./fast5/include
+FAST5_INCLUDE = -I./fast5/include
 
 # Include the header-only eigen library
-EIGEN_INCLUDE=-I./eigen/
+EIGEN_INCLUDE = -I./eigen/
 
 # Include the src subdirectories
-NP_INCLUDE=$(addprefix -I./, $(SUBDIRS))
+NP_INCLUDE = $(addprefix -I./, $(SUBDIRS))
 
 CUDA_INCLUDE=-I/usr/local/cuda-9.0/include
 
 # Add include flags
 CPPFLAGS += $(H5_INCLUDE) $(HTS_INCLUDE) $(FAST5_INCLUDE) $(NP_INCLUDE) $(EIGEN_INCLUDE) $(CUDA_INCLUDE)
 
 # Main programs to build
-PROGRAM=nanopolish
-TEST_PROGRAM=nanopolish_test
+PROGRAM = nanopolish
+TEST_PROGRAM = nanopolish_test
 
+.PHONY: all
 all: $(PROGRAM) $(TEST_PROGRAM)
 
 #
@@ -90,15 +91,20 @@ htslib/libhts.a:
 # If this library is a dependency the user wants HDF5 to be downloaded and built.
 #
 lib/libhdf5.a:
-	if [ ! -e hdf5-1.8.14.tar.gz ]; then wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.14/src/hdf5-1.8.14.tar.gz; fi
+	if [ ! -e hdf5-1.8.14.tar.gz ]; then \
+		wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.14/src/hdf5-1.8.14.tar.gz; \
+	fi
 	tar -xzf hdf5-1.8.14.tar.gz || exit 255
-	cd hdf5-1.8.14 && ./configure --enable-threadsafe --prefix=`pwd`/.. && make && make install
-
+	cd hdf5-1.8.14 && \
+		./configure --enable-threadsafe --prefix=`pwd`/.. && \
+		make && make install
 
 # Download and install eigen if not already downloaded
 eigen/INSTALL:
-	if [ ! -e 3.2.5.tar.bz2 ]; then wget http://bitbucket.org/eigen/eigen/get/3.2.5.tar.bz2; fi
-	tar -xjvf 3.2.5.tar.bz2 || exit 255
+	if [ ! -e 3.2.5.tar.bz2 ]; then \
+		wget http://bitbucket.org/eigen/eigen/get/3.2.5.tar.bz2; \
+	fi
+	tar -xjf 3.2.5.tar.bz2 || exit 255
 	mv eigen-eigen-bdd17ee3b1b3 eigen || exit 255
 
 #
@@ -109,7 +115,7 @@ eigen/INSTALL:
 CPP_SRC := $(foreach dir, $(SUBDIRS), $(wildcard $(dir)/*.cpp))
 CU_SRC := $(foreach dir, $(SUBDIRS), $(wildcard $(dir)/*.cu))
 C_SRC := $(foreach dir, $(SUBDIRS), $(wildcard $(dir)/*.c))
-EXE_SRC=src/main/nanopolish.cpp src/test/nanopolish_test.cpp
+EXE_SRC = src/main/nanopolish.cpp src/test/nanopolish_test.cpp
 
 # Automatically generated object names
 CPP_OBJ=$(CPP_SRC:.cpp=.o)
@@ -119,7 +125,7 @@ CU_OBJ=$(CU_SRC:.cu=.o)
 .SUFFIXES: .cu
 
 # Generate dependencies
-PHONY=depend
+.PHONY: depend
 depend: .depend
 
 .depend: $(CPP_SRC) $(C_SRC) $(CU_SRC) $(EXE_SRC) $(H5_LIB) $(EIGEN_CHECK)
@@ -146,8 +152,11 @@ $(PROGRAM): src/main/nanopolish.o $(CU_OBJ) $(CPP_OBJ) $(C_OBJ) $(HTS_LIB) $(H5_
 $(TEST_PROGRAM): src/test/nanopolish_test.o $(CPP_OBJ) $(CU_OBJ) $(C_OBJ) $(HTS_LIB) $(H5_LIB)
 	$(CXX) -o $@ $(CXXFLAGS) $(CPPFLAGS) -fPIC $< $(CPP_OBJ) $(CU_OBJ) $(C_OBJ) $(HTS_LIB) $(H5_LIB) $(LIBS) $(LDFLAGS) $(CURTFLAGS)
 
+.PHONY: test
 test: $(TEST_PROGRAM)
 	./$(TEST_PROGRAM)
 
+.PHONY: clean
 clean:
 	rm -f $(PROGRAM) $(TEST_PROGRAM) $(CPP_OBJ) $(CU_OBJ) $(C_OBJ) src/main/nanopolish.o src/test/nanopolish_test.o
+		src/main/nanopolish.o src/test/nanopolish_test.o

README.md

@@ -6,6 +6,8 @@ Software package for signal-level analysis of Oxford Nanopore sequencing data. N
 
 ## Release notes
 
+* 0.10.2: added new program `nanopolish polya` to estimate the length of poly-A tails on direct RNA reads (by @paultsw)
+
 * 0.10.1: `nanopolish variants --consensus` now only outputs a VCF file instead of a fasta sequence. The VCF file describes the changes that need to be made to turn the draft sequence into the polished assembly. A new program, `nanopolish vcf2fasta`, is provided to generate the polished genome (this replaces `nanopolish_merge.py`, see usage instructions below). This change is to avoid issues when merging segments that end on repeat boundaries (reported by Michael Wykes and Chris Wright).
 
 ## Dependencies

docs/source/quickstart_consensus.rst

@@ -87,13 +87,24 @@ First, we align the original reads (``reads.fasta``) to the draft assembly (``dr
 Then we run the consensus algorithm. For larger datasets we use ``nanopolish_makerange.py`` to split the draft genome assembly into 50kb segments, so that we can run the consensus algorithm on each segment in parallel. The output would be the polished segments in ``fasta`` format. 
 Since our dataset is only covering a 2kb region, we skip this step and use the following command: ::
 
-    nanopolish variants --consensus polished.fa \
+    nanopolish variants --consensus -o polished.vcf \
         -w "tig00000001:200000-202000" \
         -r reads.fasta \
         -b reads.sorted.bam \
         -g draft.fa
 
-We are left with our desired output: ``polished.fa``.
+We are left with: ``polished.vcf``.
+
+**Note**: As of v0.10.1, ``nanopolish variants --consensus`` only outputs a VCF file instead of a fasta sequence.
+
+To generate the polished genome in fasta format: ::
+
+    nanopolish vcf2fasta --skip-checks -g draft.fa polished.vcf > polished_genome.fa
+
+We only polished a 2kb region, so let's pull that out: :: 
+
+    samtools faidx polished_genome.fa
+    samtools faidx polished_genome.fa "tig00000001:200000-202000" > polished.fa
 
 Evaluate the assembly
 ---------------------------------