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= <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]]
<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]]
