NAME

       srf_filter - filter SRF files for various purposes

SYNOPSIS

       srf_filter [-c chunk_types] [-f read_filter] [-C] [-o] [-v] input(s) output

OPTIONS

       -c chunk_types

              Chunk  types to output given as a comma delimited list of types.  The following types are allowed:
              "ALL", "BASE", "CNF1", "CNF4" "SAMP", "SMP4".  The default is "ALL".

       -m mdata_types

              SAMP/SMP4 mdata types to output given as a comma delimited list of types.  The following types are
              allowed: "ALL", "PROC", "SLXI", "SLXN" "0FAM", "1CY3", "2TXR", "3CY5".  The default is "ALL".

       -f read_filter

       The filter to apply to reads in the archive.
              If reads match the

              filter they are dumped.  The filter takes the form of <name>=<value>, where <name> can be  "read",
              "prefix",  "file".   If  the  <name> is "read" the value is represents the name of a read to dump.
              Only the matching read will be dumped.  If the <name> is "prefix"  the  value  is  represents  the
              prefix  of  the name of the reads to dump.  Only the matching reads will be dumped.  If the <name>
              is "file" the value is a file name where any number of "read" and "prefix" name value pairs can be
              included, one per line.  The default is no filter, which means all reads are dumped.

       -b     exclude bad reads using readsFlags bitmask in data block header.

       -2 cyc use this option to add a Illumina-style REGN chunk.

       -v     Print verbose messages.

       Use '-' for the input or output name to read from stdin or write to stdout.

srf_filter 1.13.2                                  August 2013                                     SRF_FILTER(1)