BAM Filter: Setup, Compilation, and Usage Guide

Environment Setup

mamba create -n bamfilter bioconda::samtools bioconda::htslib zlib gcc 

Compilation

g++ -O2 -o filter_bam bam_filter.cpp -I$CONDA_PREFIX/include -L$CONDA_PREFIX/lib -lhts -lz -lpthread -Wl,-rpath,$CONDA_PREFIX/lib

Usage

Run the program with the following command:

./filter_bam input.bam output.bam MAPQ_threshold [num_threads]

• input.bam: Path to the input BAM file
• output.bam: Path for the output BAM file
• MAPQ_threshold: Minimum MAPQ value to keep a read pair
• num_threads (optional): Number of threads to use (default is 1)

Example:

./filter_bam test_reads.bam filtered_reads.bam 20 4

Example: This command filters all_reads.bam, keeping only read pairs where both reads have a MAPQ score of at least 20, using 4 threads, and saves the result to filtered_reads.bam.

Troubleshooting

If you encounter library loading errors, ensure that the Conda environment is activated and try setting the LD_LIBRARY_PATH (Linux) or DYLD_LIBRARY_PATH (macOS):

export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH  # Linux
export DYLD_LIBRARY_PATH=$CONDA_PREFIX/lib:$DYLD_LIBRARY_PATH  # macOS

Then run the program again.