Bwa-Postalt

Use C++ multi-threading parallel to speed up bwa-postalt.js for processing sam data.

Requirements

OS: centos 7+

softwares/librarys:

name	version	usage
cmake	3.14+	compile
gcc	9.1.0+	compile
CLI11	1.9.0	cmd
spdlog	1.5.0	log

Usage

Build and run the standalone target

Use the following command to build executable target.

# ./script/build.sh
cmake -Hstandalone -Bbuild/standalone
cmake --build build/standalone

To run the executable target.

cat input.sam | ./build/standalone/Bwa-Postalt input.alt > output.sam

# or

bwa mem -M -t 10 $ref $fq1 $fq2 | ./build/standalone/Bwa-Postalt input.alt > output

The program read sam data from stdin and write the sam data to stdout using pipelines of linux platform.

The detailed instructions are as follows.

$./build/standalone/Bwa-Postalt -h
Bwa-Postalt: Process sam data.
Usage: ./build/standalone/Bwa-Postalt [OPTIONS] alt file

Positionals:
  alt file TEXT:FILE REQUIRED           Position paramter

Options:
  -h,--help                             Print this help message and exit
  -c INT:POSITIVE                       Core number, default detect
  -b INT:POSITIVE                       Line number of single buffer, default 1M
  --log TEXT                            Set logging path, default './logs'

Bwa-Postalt version: 1.0.0

Build and run test suite

Use the following commands from the project's root directory to run the test suite.

# ./script/test.sh
cmake -Htest -Bbuild/test
cmake --build build/test

if [[ $? == 0 ]];
then
    echo "Compile success!"
    # CTEST_OUTPUT_ON_FAILURE=1 cmake --build build/test --target test
    # or simply call the executable: 
    ./build/test/Bwa-PostaltTests
else
    echo "Compile failed!"
fi

To collect code coverage information, run CMake with the -DENABLE_TEST_COVERAGE=1 option.

Build the documentation

The documentation is automatically built and published whenever a GitHub Release is created. To manually build documentation, call the following command.

# ./script/doc.sh
cmake -Hdocumentation -Bbuild/doc
cmake --build build/doc --target GenerateDocs
# view the docs
# open build/doc/doxygen/html/index.html

To build the documentation locally, you will need Doxygen, jinja2 and Pygments on installed your system.

Performance

Compare original JS script with C++ version

time cat $input_sam | Bwa-Postalt $alt -c 10 -b 1000000 > $output_sam


time cat $input_sam | k8 bwa-postalt.js $alt > $output_sam

The size of input sam is 64GB, and the results:

version	time(s)	memory(MB)	CPU
js	4003	653	1
c++	268	7000	5

This shows the speedup of c++ version is more than 10 times, and the bottleneck is speed of disk IO