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 PicardCollectInsertSizeMetrics
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