rnalysis.fastq.validate_sam

rnalysis.fastq.validate_sam(input_folder: Union[str, Path], output_folder: Union[str, Path], picard_installation_folder: Union[str, Path, Literal['auto']] = 'auto', verbose: bool = True, is_bisulfite_sequenced: bool = False)

Validate SAM/BAM files using Picard ValidateSamFile.

Parameters

  • input_folder (str or Path) – Path to the folder containing the SAM/BAM files you want to validate.

  • output_folder (str or Path) – Path to a folder in which the validation reports will be saved.

  • picard_installation_folder (str, Path, or 'auto' (default='auto')) – Path to the installation folder of Picard. For example: ‘C:/Program Files/Picard’

  • new_sample_names (list of str or 'auto' (default='auto')) – Give a new name to each converted sample (optional). If sample_names=’auto’, sample names will be given automatically. Otherwise, sample_names should be a list of new names, with the order of the names matching the order of the files in the directory.

  • verbose (bool (default=True)) – If True, the validation report will be verbose. If False, the validation report will be a summary.

  • is_bisulfite_sequenced (bool (default=False)) – Indicates whether the SAM/BAM file consists of bisulfite sequenced reads. If so, C->T is not counted as en error in computer the value of the NM tag.

Returns

a list of the paths to the generated FASTQ files.

Return type

list of str