smftools.informatics.bam\_functions
===================================

.. automodule:: smftools.informatics.bam_functions

   
   .. rubric:: Functions

   .. autosummary::
   
      align_and_sort_BAM
      annotate_demux_type_from_bi_tag
      annotate_umi_tags_in_bam
      bam_qc
      build_barcode_sidecar_from_split_bams
      build_classified_read_set
      concatenate_fastqs_to_bam
      count_aligned_reads
      demux_and_index_BAM
      derive_bm_from_bi_to_sidecar
      derive_umi_orientation_tags_from_aligned_bam
      extract_and_assign_barcodes_in_bam
      extract_base_identities
      extract_read_features_from_bam
      extract_read_tags_from_bam
      extract_readnames_from_bam
      extract_secondary_supplementary_alignment_spans
      find_secondary_supplementary_read_names
      load_barcode_references_from_yaml
      load_umi_config_from_yaml
      resolve_barcode_config
      resolve_umi_config
      separate_bam_by_bc
      split_and_index_BAM
      subsample_split_bams
   
   .. rubric:: Classes

   .. autosummary::
   
      BarcodeKitConfig
      FlankingConfig
      PerEndFlankingConfig
      UMIExtractionResult
      UMIKitConfig