This mode is used to display statistics about files in one of the compact Goby formats (reads or alignments). It is implemented by edu.cornell.med.icb.goby.modes.CompactFileStatsMode.java.

Mode Parameters

The following options are available in this mode

FlagArgumentsRequiredDescription
n/ainputyesThe input filenames to to get statistics for. Compact file formats are recognized (reads or alignments)
(-q|--number-of-quantiles)number-of-quantilesnoNumber of quantiles used to characterize read length distribution.
(-v|--verbose)n/anoDisplay detailed statistics.

Example Usage

$ java -jar goby.jar --mode compact-file-stats data/reads/goby-mouse-reads-sample.compact-reads
Compact reads filename = data/reads/goby-mouse-reads-sample.compact-reads
Average bytes per entry: 17.256396
Average bytes per base: 0.392191
Has identifiers    = false (0)
Has descriptions   = false (0)
Has sequences      = true (1,000,000)
Has quality scores = false (0)
Number of entries = 1,000,000
Min read length = 44
Max read length = 44
Avg read length = 44
Total number of files processed = 1
Total number of reads = 1,000,000
Min read length = 44
Max read length = 44
Avg read length = 44