Fixed issues in segment with bulk libraries.
#141
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- Added better logging in `segment` for model annotations. - `segment` now cues off the model `annotation_segments` for what annotations are required on output. - `segment` now has repeatable order for `it` tag output (READ_CLIPPED_SEQS_LIST_TAG) - Split `bam_utils.has_cbc_and_umi` into two methods. - Added two new tags for demultiplexing indices in bulk (and other) libraries. - Now `LibraryModel.has_umi_annotation` will cue off of both the raw and final UMI tags. - Now `LibraryModel.has_cell_barcode_annotation` will cue off of both the raw and final CBC tags. - Updated all models that annotate UMIs to annotate both the final and raw UMI tags. - Fixed typo in the `mas_15_bulk_10x5p_single_internal` `array_element_structure`. - Updated tests for `segment` to validate against expected output for 3 models (`mas_15_bulk_10x5p_single_internal`, `mas_10_sc_10x5p_single_none`, `mas_15_sc_10x5p_single_none`). - Added unit test file for the model.
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segmentfor model annotations.segmentnow cues off the modelannotation_segmentsfor what annotations are required on output.segmentnow has repeatable order forittag output (READ_CLIPPED_SEQS_LIST_TAG)bam_utils.has_cbc_and_umiinto two methods.LibraryModel.has_umi_annotationwill cue off of both the raw and final UMI tags.LibraryModel.has_cell_barcode_annotationwill cue off of both the raw and final CBC tags.mas_15_bulk_10x5p_single_internalarray_element_structure.segmentto validate against expected output for 3 models (mas_15_bulk_10x5p_single_internal,mas_10_sc_10x5p_single_none,mas_15_sc_10x5p_single_none).