rnalysis.fastq.fastq_to_sam_paired

rnalysis.fastq.fastq_to_sam_paired(r1_files: List[str], r2_files: List[str], output_folder: Union[str, Path], picard_installation_folder: Union[str, Path, Literal['auto']] = 'auto', new_sample_names: Union[List[str], Literal['auto']] = 'auto', output_format: Literal['sam', 'bam'] = 'bam', quality_score_type: Union[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: ‘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