Sortdep: Difference between revisions
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wget http://popgen.dk/software/download/sortDep.cpp | wget http://popgen.dk/software/download/sortDep.cpp | ||
g++ sortDep.cpp -O3 -o sortDep -lz | g++ sortDep.cpp -O3 -o sortDep -lz | ||
</pre> | |||
<pre> | |||
chr pos depth | |||
1 1 5 | |||
1 2 10 | |||
1 3 1 | |||
.... | |||
</pre> | |||
<pre> | |||
./sortDep -skip 1 -col 3 >depths | |||
</pre> | </pre> | ||
Revision as of 15:37, 19 March 2014
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