rnalysis.fastq.sam_to_fastq_single

rnalysis.fastq.sam_to_fastq_single(input_folder: str | Path, output_folder: str | Path, picard_installation_folder: str | Path | Literal['auto'] = 'auto', new_sample_names: List[str] | Literal['auto'] = 'auto', re_reverse_reads: bool = True, include_non_primary_alignments: bool = False, quality_trim: PositiveInt | None = None)

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.

  • re_reverse_reads (bool (default=True)) – Re-reverse bases and qualities of reads with the negative-strand flag before writing them to FASTQ.

  • include_non_primary_alignments (bool (default=False)) – If true, include non-primary alignments in the output. Support of non-primary alignments in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and there are paired reads with non-primary alignments.

  • quality_trim (positive int or None (default=None)) – If enabled, End-trim reads using the phred/bwa quality trimming algorithm and this quality.

Returns:

a list of the paths to the generated FASTQ files.

Return type:

list of str