This PR completely drops cellranger dependency by adding functionality to convert FASTQs to an unmapped BAM and perform (optional) barcode correction to a whitelist.
Added preprocess.pipeline.convert_fastqs_to_unmapped_bam, which converts a set of FASTQs into an unmapped BAM with the appropriate BAM tags.
Renamed preprocess.UMI_utils.sort_cellranger_bam to sort_bam.
Reordered requirements to be alphabetical in setup.py.
Remove _id argument from error_correct_umis. This argument used to be passed to UMI_utils.correct_umis_in_group, but it is not used anymore.
Update command-line pipeline to support new functionality. Renamed error_correct to error_correct_umis so that it can be differentiated with barcode correction.
Removed pandas-charm from requirements and bumped pandas>=1.1.4 and numpy>=1.19.5
This PR completely drops cellranger dependency by adding functionality to convert FASTQs to an unmapped BAM and perform (optional) barcode correction to a whitelist.
preprocess.pipeline.convert_fastqs_to_unmapped_bam, which converts a set of FASTQs into an unmapped BAM with the appropriate BAM tags.preprocess.UMI_utils.sort_cellranger_bamtosort_bam.setup.py.ngs-tools>=1.4.0as a dependency.argparsefrom requirements. As of Python 3.2, this is part of the standard library. See https://pypi.org/project/argparse/preprocess.pipeline.error_correct_barcodes. https://kb.10xgenomics.com/hc/en-us/articles/115003822406-How-does-Cell-Ranger-correct-barcode-sequencing-errors_idargument fromerror_correct_umis. This argument used to be passed toUMI_utils.correct_umis_in_group, but it is not used anymore.error_correcttoerror_correct_umisso that it can be differentiated with barcode correction.pandas-charmfrom requirements and bumpedpandas>=1.1.4andnumpy>=1.19.5