rnalysis.fastq.sort_sam

rnalysis.fastq.sort_sam(input_folder: str | Path, output_folder: str | Path, picard_installation_folder: str | Path | Literal['auto'] = 'auto', new_sample_names: List[str] | Literal['auto'] = 'auto', sort_order: Literal['coordinate', 'queryname', 'duplicate'] = 'coordinate')

Sort SAM/BAM files using Picard SortSam.

Parameters:

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

  • output_folder (str or Path) – Path to a folder in which the sorted SAM/BAM files will be saved.

  • picard_installation_folder (str, Path, or 'auto' (default='auto')) – Path to the installation folder of Picard. For example: β€˜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.

  • sort_order ('coordinate', 'queryname', or 'duplicate' (default='coordinate')) – The order in which the alignments should be sorted.