srf_filter - filter SRF files for various purposes
srf_filter [-c chunk_types] [-f read_filter]
[-C] [-o] [-v] input(s) output
-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.