Sortdep

A ultrafast and efficient tabulation of integers.

Very usefull for finding coverage and depth of coverage of sequencing data.

The functionality is similar to sort -n depths.txt |uniq -c.

Installation

wget http://popgen.dk/software/download/sortDep.cpp
g++ sortDep.cpp -O3 -o sortDep -lz

chr pos depth
1 1 5
1 2 10
1 3 1
....

./sortDep -skip 1 -col 3 >depths