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.

Problems with unix sort is that it floods the $TMPDIR. This utility program keeps the data in memory,

Installation

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

File below called depths.txt

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

./sortDep -skip 1 -col 3 depths.txt >depths
#or
cat depths.txt |./sortDepth -skip 1 -col3 >depths
#or
cat depths.txt |cut -f3 |sed 1d|./sortDepth >depths

Input as filename can be gz compressed, input as stdin are required to be uncompressed.