StatsTools
statsTools Overview
statsTools 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 - merge stats files in the Count-Based Output Format (sumStats)
- subsetBaseQCStats - reduce the stats file to just the positions in the specified regions.
mergeBaseQCSumStats
Merges stats files in the 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 (--out)
Use --out 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 - is used to indicate stdout.
| uncompressed to file | --out yourFileName.stats
|
| compressed to file | --out yourFileName.stats.gz
|
| uncompressed to stdout | --out -
|
| compressed to stdout | --out -.gz
|
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 --out).
The software can read either compressed or uncompressed stats files, but they must be in the 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.
