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SAMReader

Reads in SAM/BAM formatted files

One output contains the data the other one contains the header section of the input file.

Options

file name: SAM or BAM formatted file
limit rows: for testing purposes it is sometimes useful to limit the number of rows to read in and thereby reducing the amount of time it takes to load data and execute the workflow. If this is set to zero all lines are being read in.
Validation level: if set to strict exceptions will be produced, if set to lenient warning, and if set to silent non-conforming lines will be read but you won't be notified.

Input Ports

This node has no input ports

Output Ports

: Data table
: Header of input file. One line = one row

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Installation

To use this node in KNIME, install the extension KNIME NGS tools from the below update site following our NodePit Product and Node Installation Guide:

v4.6

A zipped version of the software site can be downloaded here.

Plugin provider: Bernd Jagla, Institute Pasteur

Plugin version: 0.2.300.qualifier

On NodePit since: 2022-06-11

Last update: 2024-04-18

KNIME versions: From v3.6 to v4.6

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