rnalysis.fastq.fastq_to_sam_paired

rnalysis.fastq.fastq_to_sam_paired(r1_files: List[str], r2_files: List[str], output_folder: str | Path, picard_installation_folder: str | Path | Literal['auto'] = 'auto', new_sample_names: List[str] | Literal['auto'] = 'auto', output_format: Literal['sam', 'bam'] = 'bam', quality_score_type: Literal['auto'] | Literal['phred33', 'phred64', 'solexa-quals', 'int-quals'] = 'auto')

Convert SAM/BAM files to FASTQ files using Picard SamToFastq.

Parameters:

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

  • output_folder (str or Path) – Path to a folder in which the converted FASTQ 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.

Returns:

a list of the paths to the generated FASTQ files.

Return type:

list of str