Tools¶

Test Tool¶

class Bam_QC.tool.bamqc.bamQC(configuration=None)[source]¶

Tool for statistical and qualitative analysis of a Bam file

bamqc(**kwargs)[source]¶

Count the number of characters in a file and return a file with the count

Parameters:	file_in_loc (str) – Location of the input file file_out_loc (str) – Location of an output file
Returns:	Writes to the file, which is returned by pyCOMPSs to the defined location
Return type:	bool

static get_bamqc_params(params)[source]¶

Function to handle for extraction of commandline parameters :param params: :type params: dict

Returns:
Return type:	list

run(input_files, input_metadata, output_files)[source]¶

The main function to run the bamqc tool

Parameters:

input_files (dict) – Input bam file
input_metadata (dict) – Matching metadata for the file, plus any additional data
output_files (dict) – html file containing reports.

Returns: