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.