Although the user could provide alternative paths for samtools and bedtools during the configuration steps, these paths were not used when making the coverage reports, resulting in errors when these tools are not directly available in the PATH. Now the user specified paths are used when generating the coverage reports.
Although the user could provide alternative paths for samtools and bedtools during the configuration steps, these paths were not used when making the coverage reports, resulting in errors when these tools are not directly available in the PATH. Now the user specified paths are used when generating the coverage reports.