---
name: "srf_filter"
section: "1"
platform: "linux"
package: "staden-io-lib-utils"
version: "1.15.0-1.1+b2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/srf_filter"
---

# srf\_filter(1)

filter SRF files for various purposes

## 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.