seqCNA C++ code to generate files for readSeqsumm
The R project can be found here: Bioconductor: seqCNA
This is the C++ code from the R package David Mosen-Ansorena published, adapted to run from the command line. I used this to generate the files used for down-steam analysis of copy number variations using the seqCNA R package as the runSeqsumm function did not work on my machine.
git clone https://github.com/davidvi/CopyNumberAnalysis.git
cd CopyNumberAnalysis
g++ copy_number_analysis.cpp -lm -o cna
./cna -s 50 -i input.bam -o output.txt
options: -s slide window size (*1000) -i input bam file -o output txt file for use in seqCNA R package