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The functionality is similar to '''sort -n depths.txt |uniq -c'''. | 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= | =Installation= | ||
<pre> | <pre> | ||
wget http://popgen.dk/software/download/sortDep.cpp | wget http://popgen.dk/software/download/sortDep.cpp | ||
g++ sortDep.cpp -O3 -o sortDep - | g++ sortDep.cpp -O3 -o sortDep -Liz | ||
</pre> | </pre> | ||
File below called depths.txt | |||
<pre> | |||
chr pos depth | |||
1 1 5 | |||
1 2 10 | |||
1 3 1 | |||
.... | |||
</pre> | |||
<pre> | |||
./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 | |||
</pre> | |||
;Input as filename can be gz compressed, input as stdin are required to be uncompressed. | |||
Latest revision as of 14:45, 20 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.
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.