comparison srf2fastq/io_lib-1.12.2/man/man1/srf_info.1 @ 0:d901c9f41a6a default tip

Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository

0:d901c9f41a6a

.TH srf_info 1 "September 19" "" "Staden io_lib"

.SH "NAME"

.PP
.BR srf_info
\- Lists information about the contents of an SRF file

.SH "SYNOPSIS"
.PP
\fBsrf_info\fR  [\fI-l\fR bitmap] \fIsrf_archive\fR ...

.SH "DESCRIPTION"
.PP
\fBsrf_info\fR lists some simple frequency metrics on the contents of
an SRF file, both in terms of how many traces there are and the sort of
data held within them.
.PP
For efficiencies sake some control is given over which statistics to
gather and display. This is controlled by the \fI-l\fR level
parameter. The value is the summation of one or more of the following
values, representing the data to display.

.TP
1
Count of good/bad reads.
.TP
2
Counts and compressed size for selected chunk types.
.TP
4
Trace count and trace name prefix for each trace_header.
.TP
8
Base count.

.SH "OPTIONS"
.PP
.TP
\fB-l\fR bitmap
Controls which statistics to gather and display. Bitmap is a value
from 0 to 15 (1+2+4+8) as described in the DESCRIPTION section above.

.SH "EXAMPLES"
.PP
To count the total number of good and bad reads along with a break
down of trace names per SRF data-block-header we would use bitmap
values 1 and 4 combined.
.PP
.nf
    srf_info -l 5 foo.srf
.fi

.PP
To count the total number of reads for all srf files in a directory.
.PP
.nf
    srf_info -l 1 *.srf
.fi

.SH "AUTHOR"
.PP
Steven Leonard, Wellcome Trust Sanger Institute