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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 se- quences 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 in- formation on the position in the archive and the size of the se- quence 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)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | EXAMPLES | AUTHOR
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