Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each allele [ACGT] at that location (given any filter settings)
Overlapping read from the same pair are becoming a common feature of modern NGS sequencing.
Prototype changes in the perl version to be compared against the eventual C one.
Any read that disagrees with it's mate at the same position should be counted for each allele and double counted for depth so no bias occurs.
e.g.
#Read of pair agree at same position
Read 1 = A
Read 2 = A
Results in: Allele_A = 1, depth = 1
#Read of pair DISagree at same position
Read 1 = A
Read 2 = T
Results in: Allele_A = 1, Allele_T = 1, depth = 2
Overlapping read from the same pair are becoming a common feature of modern NGS sequencing.
Prototype changes in the perl version to be compared against the eventual C one.
Any read that disagrees with it's mate at the same position should be counted for each allele and double counted for depth so no bias occurs.
e.g.