StatsTools - Revision history

Mktrost at 21:17, 1 June 2012

2012-06-01T21:17:23Z

← Older revision		Revision as of 17:17, 1 June 2012
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	== Parameters ==		== Parameters ==
			<pre>
	--out output merged stats file		--out output merged stats file
	inputStatsFiles space separated list of files to merge.		inputStatsFiles space separated list of files to merge.
			</pre>

	=== output File (<code>--out</code>) ===		=== output File (<code>--out</code>) ===
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	== Parameters ==		== Parameters ==
			<pre>
	--inStats : stats file to narrow down to just a subset of positions		--inStats : stats file to narrow down to just a subset of positions
	--regionList : File containing the subset of regions to keep (assumed to be sorted)		--regionList : File containing the subset of regions to keep (assumed to be sorted)
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	Positions are 0 based and the end_pos is not included in the region.		Positions are 0 based and the end_pos is not included in the region.
	--outStats : stats file to write the subset of stats into		--outStats : stats file to write the subset of stats into
			</pre>

	=== input File (<code>--inStats</code>) ===		=== input File (<code>--inStats</code>) ===

Mktrost at 19:56, 28 November 2011

2011-11-28T19:56:23Z

← Older revision		Revision as of 15:56, 28 November 2011
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	\| 0-based region end position (not included in the output file).		\| 0-based region end position (not included in the output file).
	\|}		\|}


	=== output File (<code>--outStats</code>) ===		=== output File (<code>--outStats</code>) ===
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	== Return Value ==		== Return Value ==
	The software returns 0 on completion, or -~~1 if the parameters could not be read or there was~~ a ~~problem reading an input file~~.		The software returns 0 on successful completion, or non-zero on a failure.

	== Output ==		== Output ==
	~~A status message is~~ written to cerr ~~on failures~~, ~~and upon completion~~, "~~Done writing to~~ " followed by the ~~output file name~~ is written to cerr.		Status/error messages are written to cerr.

			If an invalid region is found in the regionList, "NonOverlapRegionPos::add: Invalid Range, start must be < end, but ", followed by the start position, followed by " >= ", followed by the end position.

			Upon completion, "Done subsetBaseQCStats." is written to cerr.

			'''Example Output:'''
			NonOverlapRegionPos::add: Invalid Range, start must be < end, but 112 >= 111
			Done subsetBaseQCStats.


	[[Category:BAM_Software]] [[Category:Software]]		[[Category:BAM_Software]] [[Category:Software]]

Mktrost at 19:48, 28 November 2011

2011-11-28T19:48:58Z

@@ Line 45: / Line 45: @@
 == Return Value ==
-The software returns 0 on success, non-0 on failure.
+The software returns 0 on completion, or -1 if the parameters could not be read or there was a problem reading an input file.
 == Output ==
-A status message is written to cerr on failures, and upon successful completion, "Done writing to " followed by the output file name is written to cerr.
+A status message is written to cerr on failures, and upon completion, "Done writing to " followed by the output file name is written to cerr.
 [[Category:BAM_Software]] [[Category:Software]]

Mktrost: Created page with '= `statsTools` Overview = `statsTools` contains a set of tools for operating on the statistics files that we generate. Currently it only works on baseQC st…'

2011-11-28T19:22:36Z

Created page with '= <code>statsTools</code> Overview = <code>statsTools</code> contains a set of tools for operating on the statistics files that we generate. Currently it only works on baseQC st…'

New page

= <code>statsTools</code> Overview =
<code>statsTools</code> contains a set of tools for operating on the statistics files that we generate.

Currently it only works on baseQC statistics files produced by [[BamUtil: stats]].
* [[#mergeBaseQCSumStats|mergeBaseQCSumStats]] - merge stats files in the Count-Based Output Format (sumStats)
* [[#subsetBaseQCStats|subsetBaseQCStats]] - reduce the stats file to just the positions in the specified regions.

= mergeBaseQCSumStats =
Merges stats files in the [[BamUtil:_stats#Count-Based_Output_Format|Count-Based Output Format]].

The merge can be done in multiple iterations, merging smaller groups of files at a time.

==Usage==
mergeBaseQCSumStats --out <outputStatsFile> <inputStatsFiles>

== Parameters ==
--out output merged stats file
inputStatsFiles space separated list of files to merge.

=== output File (<code>--out</code>) ===

Use <code>--out</code> followed by your file name to specify the merged stats output file.

The file extension is used to determine whether or not to compressed the output file. A <code>-</code> is used to indicate stdout.

{|border="1" cellspacing="0" cellpadding="2"
|uncompressed to file
| <code>--out yourFileName.stats</code>
|-
|compressed to file
| <code>--out yourFileName.stats.gz</code>
|-
|uncompressed to stdout
| <code>--out -</code>
|-
|compressed to stdout
| <code>--out -.gz</code>
|}

=== input Stats Files ===

The input stats files to merge do not have a flag, and are just specified at the end of the command line (after <code>--out</code>).

The software can read either compressed or uncompressed stats files, but they must be in the [[BamUtil:_stats#Count-Based_Output_Format|Count-Based Format]].

== Return Value ==
The software returns 0 on success, non-0 on failure.

== Output ==
A status message is written to cerr on failures, and upon successful completion, "Done writing to " followed by the output file name is written to cerr.

[[Category:BAM_Software]] [[Category:Software]]

StatsTools - Revision history

Mktrost at 21:17, 1 June 2012

Mktrost at 19:56, 28 November 2011

Mktrost at 19:48, 28 November 2011

Mktrost: Created page with '= statsTools Overview = statsTools contains a set of tools for operating on the statistics files that we generate. Currently it only works on baseQC st…'

Mktrost: Created page with '= `statsTools` Overview = `statsTools` contains a set of tools for operating on the statistics files that we generate. Currently it only works on baseQC st…'