Sortdep - Revision history

Thorfinn at 13:45, 20 March 2014

2014-03-20T13:45:01Z

← Older revision		Revision as of 15:45, 20 March 2014
Line 5:		Line 5:
	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 '''$TMPDIR''. This utility program keeps the data in memory,		Problems with unix sort is that it floods the ''$TMPDIR''. This utility program keeps the data in memory,

	=Installation=		=Installation=

2014-03-19T14:43:53Z

Installation

← Older revision		Revision as of 16:43, 19 March 2014
Line 30:		Line 30:
	#or		#or
	cat depths.txt \|cut -f3 \|sed 1d\|./sortDepth >depths		cat depths.txt \|cut -f3 \|sed 1d\|./sortDepth >depths
			</pre>

	~~</pre>~~		;Input as filename can be gz compressed, input as stdin are required to be uncompressed.

2014-03-19T14:43:17Z

← Older revision		Revision as of 16:43, 19 March 2014
Line 5:		Line 5:
	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 -lz		g++ sortDep.cpp -O3 -o sortDep -Liz
	</pre>		</pre>

Line 25:		Line 26:
	<pre>		<pre>
	./sortDep -skip 1 -col 3 depths.txt >depths		./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>		</pre>

2014-03-19T14:39:42Z

Installation

← Older revision		Revision as of 16:39, 19 March 2014
Line 13:		Line 13:


			File below called depths.txt
	<pre>		<pre>
	chr pos depth		chr pos depth
Line 23:		Line 24:

	<pre>		<pre>
	./sortDep -skip 1 -col 3 >depths		./sortDep -skip 1 -col 3 depths.txt >depths
	</pre>		</pre>

2014-03-19T14:37:39Z

Installation

@@ Line 10: / Line 10: @@
 wget http://popgen.dk/software/download/sortDep.cpp
 g++ sortDep.cpp -O3 -o sortDep -lz
 </pre>

2014-03-19T14:35:51Z

Installation

← Older revision		Revision as of 16:35, 19 March 2014
Line 8:		Line 8:
	=Installation=		=Installation=
	<pre>		<pre>
			wget http://popgen.dk/software/download/sortDep.cpp
			g++ sortDep.cpp -O3 -o sortDep -lz
	</pre>		</pre>

2014-03-19T14:34:57Z

← Older revision		Revision as of 16:34, 19 March 2014
Line 4:		Line 4:

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


			=Installation=
			<pre>

			</pre>

2014-03-19T14:09:34Z

← Older revision		Revision as of 16:09, 19 March 2014
Line 3:		Line 3:
	Very usefull for finding coverage and depth of coverage of sequencing data.		Very usefull for finding coverage and depth of coverage of sequencing data.

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

2014-03-19T14:09:26Z

← Older revision		Revision as of 16:09, 19 March 2014
Line 1:		Line 1:
	A ultrafast and efficient tabulation of integers.		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 \|uniq -c'''.

2014-03-19T14:08:06Z

Created page with "A ultrafast and efficient tabulation of integers."

New page

A ultrafast and efficient tabulation of integers.