FindXmlFeatures

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FindXmlFeatures
Function XML
Phase Input
Standard CLAs GDB, NO_HEADER
Special CLAs XML_DIR, KEY, FEATURES
Source location ARACHNE_DIR/fix_input

The module FindXmlFeatures is a tool to help you create the configuration file. Its main purpose is to identify and highlight any missing trace information in the XML ancillary files, so that you can create rules in the configuration file to compensate for this missing information.

Run FindXmlFeatures XML_DIR=traceinfo. It will parse all XML files in traceinfo and list key-feature pairs in output. It will be helpful to redirect this output to a file so that you can refer back to it later. The output will describe all input libraries, and give information about the availability of XML tags for the reads in each library. If the reads in a library are missing an essential tag, they will be automatically discarded. However, if you know what the value of the feature should be, you can create a rule in the configuration file that will compensate for the missing information.

The argument FEATURES controls which features are listed in output. It defaults to "{seq_lib_id,library_id,insert_size,insert_stdev}".

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