count the number of times a kmer is present in a region

count the number of times a kmer is present in a region

count_kmer(bam, index, reg, kmer)

Arguments

bam	the cram/bam/sam file
index	the index of the cram/bam/sam file
reg	the region of interest, typically in format of chr1:start-begin
kmer	the substring to search for in the reads

Value

a dataframe with the sequnce reads and counts of the given kmer per read (i.e. two columns)

Examples

# NOT RUN {
count_kmer(bam, index, "chr1:10001-100050", "TTACGG")
# }