This is the command srf_filter that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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.
Use srf_filter online using onworks.net services
