Manuscript update

.gitignore

@@ -7,10 +7,6 @@
 *.o
 *.obj
 
-# SWIG files
-src/swig_wrapper.cpp
-lib/contextsv.py
-
 # Pycache
 __pycache__/
 
@@ -50,12 +46,8 @@ __pycache__/
 *.code-workspace
 CMakeSettings.json
 
-# Shell scripts
-*.sh
-
 # Output folder
 output/
-python/
 
 # Doxygen
 docs/html/
@@ -64,8 +56,6 @@ docs/html/
 *.sif
 
 # Test directories
-python/dbscan
-python/agglo
 linktoscripts
 tests/data
 tests/cpp_module_out
@@ -85,11 +75,6 @@ data/sv_scoring_dataset/
 data/hg38ToHg19.over.chain.gz
 data/hg19ToHg38.over.chain.gz
 
-# Test images
-python/dbscan_clustering*.png
-python/dist_plots
-upset_plot*.png
-
 # Temporary files
 lib/.nfs*
 valgrind.log

Dockerfile

@@ -6,16 +6,24 @@ ARG CONTEXTSV_VERSION
 
 WORKDIR /app
 
-RUN apt-get update
-RUN conda update conda
+RUN apt-get update && apt-get install -y --no-install-recommends ca-certificates && rm -rf /var/lib/apt/lists/*
+RUN conda update -y conda
+
+# Install ContextSV and plotting dependencies.
+RUN conda config --add channels wglab \
+	&& conda config --add channels conda-forge \
+	&& conda config --add channels bioconda \
+	&& conda create -y -n contextsv python=3.10 \
+	&& conda install -y -n contextsv -c wglab -c conda-forge -c bioconda \
+	   contextsv=${CONTEXTSV_VERSION} plotly python-kaleido \
+	&& conda clean -afy
+
+# Smoke test both commands at build time.
+RUN conda run -n contextsv contextsv --help \
+	&& conda run -n contextsv contextsv-cnv-plot --help
 
-# Install ContextSV
-RUN conda config --add channels wglab
-RUN conda config --add channels conda-forge
-RUN conda config --add channels bioconda
-RUN conda create -n contextsv python=3.9
-RUN echo "conda activate contextsv" >> ~/.bashrc
 SHELL ["/bin/bash", "--login", "-c"]
-RUN conda install -n contextsv -c wglab -c conda-forge -c bioconda contextsv=${CONTEXTSV_VERSION} && conda clean -afy
 
-ENTRYPOINT ["conda", "run", "--no-capture-output", "-n", "contextsv", "contextsv"]
+# Default command remains contextsv, but this allows overriding with contextsv-cnv-plot.
+ENTRYPOINT ["conda", "run", "--no-capture-output", "-n", "contextsv"]
+CMD ["contextsv"]

Doxyfile

@@ -1063,15 +1063,15 @@ EXCLUDE_SYMLINKS       = NO
 # Note that the wildcards are matched against the file with absolute path, so to
 # exclude all test directories for example use the pattern */test/*
 
-EXCLUDE_PATTERNS       = *test* *swig* khmm.cpp kc.cpp khmm.h kc.h
+EXCLUDE_PATTERNS       = *test* khmm.cpp kc.cpp khmm.h kc.h
 
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
 # (namespaces, classes, functions, etc.) that should be excluded from the
 # output. The symbol name can be a fully qualified name, a word, or if the
 # wildcard * is used, a substring. Examples: ANamespace, AClass,
 # ANamespace::AClass, ANamespace::*Test
 
-EXCLUDE_SYMBOLS        = *SWIG*
+EXCLUDE_SYMBOLS        =
 
 # The EXAMPLE_PATH tag can be used to specify one or more files or directories
 # that contain example code fragments that are included (see the \include

Makefile

@@ -11,23 +11,25 @@ CONDA_LIB_DIR := $(CONDA_PREFIX)/lib
 
 # Compiler and Flags
 CXX := g++
-CXXFLAGS := -std=c++17 -g -I$(INCL_DIR) -I$(CONDA_INCL_DIR) -Wall -Wextra -pedantic
+CXXFLAGS := -std=c++17 -O3 -DNDEBUG -I$(INCL_DIR) -I$(CONDA_INCL_DIR) -Wall -Wextra -pedantic
 
 # Linker Flags
 # Ensure that the library paths are set correctly for linking
 LDFLAGS := -L$(LIB_DIR) -L$(CONDA_LIB_DIR) -Wl,-rpath=$(CONDA_LIB_DIR)  # Add rpath for shared libraries
 LDLIBS := -lhts  # Link with libhts.a or libhts.so
 
 # Sources and Output
-SOURCES := $(filter-out $(SRC_DIR)/swig_wrapper.cpp, $(wildcard $(SRC_DIR)/*.cpp))  # Filter out the SWIG wrapper from the sources
+SOURCES := $(wildcard $(SRC_DIR)/*.cpp)
 OBJECTS := $(patsubst $(SRC_DIR)/%.cpp,$(BUILD_DIR)/%.o,$(SOURCES))
 TARGET := $(BUILD_DIR)/contextsv
+PREFIX ?= $(CONDA_PREFIX)
+BINDIR ?= $(PREFIX)/bin
 
 # Default target
 all: $(TARGET)
 
 # Debug target
-debug: CXXFLAGS += -DDEBUG
+debug: CXXFLAGS := -std=c++17 -g -O0 -DDEBUG -I$(INCL_DIR) -I$(CONDA_INCL_DIR) -Wall -Wextra -pedantic
 debug: all
 
 # Link the executable
@@ -43,3 +45,13 @@ $(BUILD_DIR)/%.o: $(SRC_DIR)/%.cpp
 # Clean the build directory
 clean:
 	rm -rf $(BUILD_DIR)
+
+# Install binaries and helper scripts
+install: $(TARGET)
+	@if [ -z "$(PREFIX)" ]; then \
+		echo "Error: PREFIX is empty. Activate a conda env or run 'make install PREFIX=/your/prefix'."; \
+		exit 1; \
+	fi
+	install -d $(BINDIR)
+	install -m 755 $(TARGET) $(BINDIR)/contextsv
+	install -m 755 python/cnv_plots_json.py $(BINDIR)/contextsv-cnv-plot

README.md

@@ -16,65 +16,120 @@ Class documentation is available at <a href="https://wglab.openbioinformatics.or
 ### Anaconda
 First, install [Anaconda](https://www.anaconda.com/).
 
-Next, create a new environment. This installation has been tested with Python 3.9, Linux 64-bit.
+Next, create a new environment. This installation has been tested with Python 3.10, Linux 64-bit.
 
-```
-conda create -n contextsv python=3.9
+```bash
+conda create -n contextsv python=3.10
 conda activate contextsv
 ```
 
 ContextSV and its dependencies can then be installed using the following command:
 
-```
+```bash
 conda install -c wglab -c conda-forge -c bioconda contextsv
+
+# Or using mamba (faster dependency resolution):
+mamba install -c wglab contextsv
+```
+
+After installation, you should have access to the following commands in your terminal:
+
+- `contextsv`: the main SV caller
+- `contextsv-cnv-plot`: utility to generate CNV plots from ContextSV JSON output
+- `contextscore`: [ContextScore](https://github.com/WGLab/ContextScore) utility for post-filtering of low-confidence SV calls
+
+Example usage:
+
+```bash
+# SV calling example:
+contextsv \
+  --bam sample.bam \
+  --ref hg38.fa \
+  --outdir output/ \
+  --threads 4 \
+  --snp snps.vcf \
+  --eth nfe \
+  --pfb gnomadv4_filepaths.txt \
+  --assembly-gaps hg38-gaps.bed \   # optional: assembly gaps file
+  --save-cnv                        # optional: save CNV calls in JSON
+
+# SV post-filtering example:
+contextscore \
+  --input input.vcf \
+  --output scored.vcf \
+  --sample-coverage 30 \
+  --buildver hg38 \
+  --threshold 0.2 \
+  --annovar /path/to/annovar \
+  --annovar-db /path/to/humandb
+
+
+# CNV plotting example:
+contextsv-cnv-plot ./output/CNVCalls.json chr3 --formats html,svg --output-dir ./CNV_Plots
 ```
 
 ### Docker
 First, install [Docker](https://docs.docker.com/engine/install/).
 Pull the latest image from Docker hub, which contains the latest release and its dependencies.
 
-```
+```bash
 docker pull genomicslab/contextsv
 ```
 
+Example usage:
+
+```bash
+# SV calling:
+docker run --rm genomicslab/contextsv --help
+
+# SV post-filtering:
+docker run --rm \
+  -v /path/to/data:/mnt \
+  genomicslab/contextsv \
+  contextscore \
+  --help
+
+# CNV plotting:
+docker run --rm \
+  -v /path/to/data:/mnt \
+  genomicslab/contextsv \
+  contextsv-cnv-plot \
+  --help
+```
+
 
 ## Building from source (for testing/development)
 ContextSV requires HTSLib as a dependency that can be installed using  [Anaconda](https://www.anaconda.com/). Create an environment
 containing HTSLib: 
 
-```
+```bash
 conda create -n htsenv -c bioconda -c conda-forge htslib
 conda activate htsenv
 ```
 
 Then follow the instructions below to build ContextSV:
 
-```
+```bash
 git clone https://github.com/WGLab/ContextSV
 cd ContextSV
 make
 ```
 
 ContextSV can then be run:
-```
+```bash
 ./build/contextsv --help
 
-Usage: ./build/contextsv [options]
 Options:
   -b, --bam <bam_file>          Long-read BAM file (required)
   -r, --ref <ref_file>          Reference genome FASTA file (required)
-  -s, --snp <vcf_file>          SNPs VCF file (required)
+  -s, --snp <vcf_file>          Long-read SNP VCF file (required)
   -o, --outdir <output_dir>     Output directory (required)
-  -c, --chr <chromosome>        Chromosome
-  -t, --threads <thread_count>  Number of threads
-  -h, --hmm <hmm_file>          HMM file
-  -n, --sample-size <size>      Sample size for HMM predictions
-     --min-cnv <min_length>     Minimum CNV length
-     --eps <epsilon>             DBSCAN epsilon
-     --min-pts-pct <min_pts_pct> Percentage of mean chr. coverage to use for DBSCAN minimum points
-  -e, --eth <eth_file>          ETH file
-  -p, --pfb <pfb_file>          PFB file
-     --save-cnv                 Save CNV data
+  -t, --threads <thread_count>  Number of threads, chromosome-level parallelization (default: 1)
+  -h, --hmm <hmm_file>          HMM parameter file for copy number predictions (included in the repository)
+  -e, --eth <eth_file>          Ethnicity as used in gnomAD (e.g. "asj" for Ashkenazi Jewish, "nfe" for Non-Finnish European, etc.)
+  -p, --pfb <pfb_file>          File containing per-chromosome population allele frequency filepaths as described in this documentation
+     --assembly-gaps <gaps_file> Assembly gaps file in BED format available from UCSC Genome Browser (https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/gap.txt.gz for GRCh38)
+     --save-cnv                 Save CNV data in JSON for downstream plotting with contextsv-cnv-plot
      --debug                    Debug mode with verbose logging
      --version                  Print version and exit
   -h, --help                    Print usage and exit
@@ -95,7 +150,7 @@ Download links for genome VCF files are located here (last updated April 3,
 
 
 ### Script for downloading gnomAD VCFs
-```
+```bash
 download_dir="~/data/gnomad/v4.0.0/"
 
 chr_list=("1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13" "14" "15" "16" "17" "18" "19" "20" "21" "22" "X" "Y")
@@ -110,7 +165,7 @@ Finally, create a text file that specifies the chromosome and its corresponding
 gnomAD filepath. This file will be passed in as an argument:
 
 **gnomadv4_filepaths.txt**
-```
+```bash
 1=~/data/gnomad/v4.0.0/gnomad.genomes.v4.0.sites.chr1.vcf.bgz
 2=~/data/gnomad/v4.0.0/gnomad.genomes.v4.0.sites.chr2.vcf.bgz
 3=~/data/gnomad/v4.0.0/gnomad.genomes.v4.0.sites.chr3.vcf.bgz

conda/build.sh

@@ -0,0 +1,31 @@
+#!/bin/bash
+
+set -e
+
+echo "Building ContextSV..."
+export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${PREFIX}/lib
+export CONDA_PREFIX=$PREFIX
+export CXXFLAGS="-I$PREFIX/include $CXXFLAGS"
+export LDFLAGS="-L$PREFIX/lib $LDFLAGS"
+
+echo "Checking for HTSLib..."
+ls -la $PREFIX/include/htslib/ || echo "HTSLib headers not found"
+pkg-config --exists htslib && echo "✓ HTSLib found" || echo "⚠ HTSLib not via pkg-config"
+
+echo "Compiling ContextSV..."
+make
+
+echo "Installing ContextSV..."
+mkdir -p ${PREFIX}/bin
+cp build/contextsv ${PREFIX}/bin/
+chmod +x ${PREFIX}/bin/contextsv
+cp python/cnv_plots_json.py ${PREFIX}/bin/contextsv-cnv-plot
+chmod +x ${PREFIX}/bin/contextsv-cnv-plot
+
+echo "Verifying ContextSV installation..."
+$PREFIX/bin/contextsv --help
+$PREFIX/bin/contextsv --version
+
+echo "Verifying CNV plotting command installation..."
+test -x ${PREFIX}/bin/contextsv-cnv-plot
+${PREFIX}/bin/contextsv-cnv-plot --help

conda/meta.yaml

@@ -10,6 +10,7 @@ source:
   git_lfs: false
 
 channels:
+  - wglab
   - conda-forge
   - bioconda
   - defaults
@@ -25,12 +26,18 @@ requirements:
     - htslib=1.20
   run:
     - htslib=1.20
+    - contextscore
+    - python >=3.9
+    - plotly
+    - python-kaleido
 
 test:
     commands:
-        - contextsv --help
-        - test -f $PREFIX/bin/contextsv
-        - contextsv --version
+    - test -x $PREFIX/bin/contextsv
+    - $PREFIX/bin/contextsv --help
+    - $PREFIX/bin/contextsv --version
+    - test -x $PREFIX/bin/contextsv-cnv-plot
+    - $PREFIX/bin/contextsv-cnv-plot --help
 about:
   home: https://github.com/WGLab/ContextSV
   license: MIT

include/fasta_query.h

@@ -24,7 +24,7 @@ class ReferenceGenome {
     public:
 	    ReferenceGenome(std::shared_mutex& shared_mutex) : shared_mutex(shared_mutex) {}
 
-        int setFilepath(std::string fasta_filepath);
+        int read(std::string fasta_filepath);
         std::string getFilepath() const;
         std::string_view query(const std::string& chr, uint32_t pos_start, uint32_t pos_end) const;
         bool compare(const std::string& chr, uint32_t pos_start, uint32_t pos_end, const std::string& compare_seq, float match_threshold) const;