This application writes out summary metrics similar to the SAV summary tab.

Running the Program

The program runs as follows:

 $ summary 140131_1287_0851_A01n401drr

In this sample, 140131_1287_0851_A01n401drr is a run folder and the summary is written to the standard output.

Note that an exhausive list of metrics can be found here: https://support-docs.illumina.com/SW/SAV/Content/SW/SAV/Metrics.htm

The InterOp sub folder may contain any of the following files:

ErrorMetricsOut.bin
ExtractionMetricsOut.bin
QMetricsOut.bin
TileMetricsOut.bin

The run folder should have:

RunInfo.xml
RunParameters.xml (This is optional for later platforms)

Error Handling

The summary program will print an error to the error stream and return an error code (any number except 0) when an error occurs. There are two likely errors that may arise:

1. The InterOp path was incorrect
2. The InterOp files do not contain valid data

A missing InterOp file will be silently ignored. Incomplete InterOp files are also ignored.