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srf_list(1) Staden io_lib srf_list(1)
NAME
srf_list - Lists and/or counts the contents of an SRF file
SYNOPSIS
srf_list [options] srf_archive ...
DESCRIPTION
srf_list lists the filenames held within one or more SRF container. To
simply count the contents rather than list them specify the -c 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 file‐
names.
Note that it is not possible to count sequences matching certain pat‐
terns or with specific flags set. srf_info is a more general purpose
tool that may cover this.
OPTIONS
-c Counts sequences instead of listing them. Note that this may be
substantially faster than listing if an index exists.
-v Verbose mode. This gives summary count information per file
rather than just the total at the end.
-l Long format. When listing sequence names this also provides
information on the position in the archive and the size of the
sequence specific data block and the size of the shared data
block header.
EXAMPLES
To count the total number of sequences in several SRF files:
srf_list -c *.srf
To produce a "fofn" (file of filenames) for an SRF file:
srf_list foo.srf > foo.fofn
AUTHOR
James Bonfield, Wellcome Trust Sanger Institute
September 29 srf_list(1)
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