IO¶
Functions related to reading and writing CySeq data.
read_cyseq_alignment_file(file, only_successful=True)
¶
Read the data from a CySeq sam or bam file.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
file
|
Path | str
|
sam or bam file to read |
required |
only_successful
|
bool
|
skip reads that failed CySeq quality control. For example, consensus was not generated, or did not align to the reference genome. |
True
|
Raises:
| Type | Description |
|---|---|
ValueError
|
if the given file does not end in |
NotImplementedError
|
if only_successful is false. |
Yields:
| Type | Description |
|---|---|
AlignmentGroup
|
An |