Pseudocode of trimming algorithm. Pseudocode of the trimming algorithm of ChopSticks. Here, L is the length of the deletion call being processed, k is a threshold used to discriminate high-coverage regions from low-coverage ones, and f is a parameter that determines the threshold of the coverage of regions to be trimmed. The variable x represents the position of the base being examined, and the variable y represents the length of a region to be trimmed. The value c[x] is the coverage at the x-th base in the deletion call, while s keeps the sum of c[x] values.