Sortdep

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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