auto_process_ngs.qc.picard

class auto_process_ngs.qc.picard.CollectInsertSizeMetrics(metrics_file)

Wrapper class for outputs from CollectInsertSizeMetrics

The CollectInsertSizeMetrics object gives access to various aspects of the outputs of the Picard CollectInsertSizeMetrics utility.

The following properties are available:

• metrics (dict): dictionary mapping metrics to values

• histogram (dict): dictionary holding histogram data

property histogram

Histogram data for insert sizes

Dictionary mapping insert sizes (keys) to associated number of alignments.

property metrics

Dictionary mapping metrics to values

To get the value associated with a metric, use e.g.:

>>> mean = insertsizes.metrics['MEAN_INSERT_SIZE']

To see what metrics are available, use e.g.:

>>> insertsizes.metrics.keys()

property metrics_file

Return path to source metrics file