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== Return Value ==
== 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 ==
== 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.
= subsetBaseQCStats =
Reduce the [[BamUtil:_stats#BaseQC|BAM BaseQC]] stats files in the to only positions in the specified regions.
==Usage==
subsetBaseQCStats --inStats <originalStatsFile> --regionList <subset of regions> --outStats <outputStatsFile>
== Parameters ==
--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)
Formated as chr<tab>start_pos<tab>end_pos.
Positions are 0 based and the end_pos is not included in the region.
--outStats : stats file to write the subset of stats into
=== input File (<code>--inStats</code>) ===
The input stats files that needs to be narrowed down to just a subset of regions.
The software can read either compressed or uncompressed stats files, but they must be in a [[BamUtil:_stats#BaseQC|BAM BaseQC format]].
=== region List File (<code>--regionList</code>) ===
The file containing the list of regions to keep from the input stats file.
The regions should be specified, one region per line.
Each column is separated by tabs.
{|border="1" cellspacing="0" cellpadding="2"
! Column # !! Description
|-
| 1
| Chromosome as written in the stats file.
|-
| 2
| 0-based region start position (included in the output file).
|-
| 3
| 0-based region end position (not included in the output file).
|}
=== output File (<code>--outStats</code>) ===
Use <code>--outStats</code> followed by your file name to specify the output file for the subset of stats.
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>
|}
== 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.
== 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.
[[Category:BAM_Software]] [[Category:Software]]
[[Category:BAM_Software]] [[Category:Software]]
