annotate srf2fastq/io_lib-1.12.2/man/man1/srf_list.1 @ 0:d901c9f41a6a default tip

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

.TH srf_list 1 "September 29" "" "Staden io_lib"

.SH "NAME"

.PP
.BR srf_list
\- Lists and/or counts the contents of an SRF file

.SH "SYNOPSIS"
.PP
\fBsrf_list\fR  [\fIoptions\fR] \fIsrf_archive\fR ...

.SH "DESCRIPTION"
.PP
\fBsrf_list\fR lists the filenames held within one or more SRF
container.  To simply count the contents rather than list them specify
the \fB-c\fR option. Note that when in count-only mode if an index is
present it will be used to determine the number of entries in the
index and hence sequences in the SRF file. The index cannot be used
when listing the filenames however as the index itself does not
contain the full filenames.
.PP
Note that it is not possible to count sequences matching certain
patterns or with specific flags set. \fBsrf_info\fR is a more general
purpose tool that may cover this.

.SH "OPTIONS"
.PP
.TP
\fB-c\fR
Counts sequences instead of listing them. Note that this may be
substantially faster than listing if an index exists.
.TP
\fB-v\fR
Verbose mode. This gives summary count information per file rather
than just the total at the end.
.TP
\fB-l\fR
Long format. When listing sequence names this also provides
information on the position in the archive and the size of the
sequence specific \fIdata block\fR and the size of the shared \fIdata
block header\fR.

.SH "EXAMPLES"
.PP
To count the total number of sequences in several SRF files:
.PP
.nf
    srf_list -c *.srf
.fi

.PP
To produce a "fofn" (file of filenames) for an SRF file:
.PP
.nf
    srf_list foo.srf > foo.fofn
.fi

.SH "AUTHOR"
.PP
James Bonfield, Wellcome Trust Sanger Institute