StatsTools

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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

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.