Generate the SAV Indexing Table

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

Running the Program

The program runs as follows:

 $ index-summary 11115124_11854Unbin2R2I

In this sample, 11115124_11854Unbin2R2I is a run folder and the summary is written to the standard output as follows

 # Version: v1.0.4-224-gacc6c8e
 Lane 1
 Total Reads     PF Reads        % Read Identified (PF) CV              Min             Max
 22855008        19391826        96.7232         0.5136          0.0001          2.9831
 Index Number    Sample Id       Project         Index 1 (I7)    Index 2 (I5)    % Read Identified (PF)
 1               AF_1-5_spike    NA              AAGAGGCA        AAGGAGTA        1.2232
 2               WU_1_spike      NA              AAGAGGCA        ACTGCATA        1.5316

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

  • IndexMetricsOut.bin
  • TileMetricsOut.bin

The run folder should have:

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

Error Handling

The index-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.