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    Uݢg                     @   s  d Z ddlZddlmZ ejejedZejedZ	dZ
dZdZd	Zd
ZdZdZdZdZdZdZdZdZdZdZdZdZdZdZdZdZdZdZ dZ!dZ"dZ#d Z$d!Z%d"Z&d#Z'd$Z(d%Z)d&Z*e)e*gZ+d'Z,d(Z-e.e/dd)d*Z0d+Z1d,Z2d-Z3d.Z4d/Z5d0Z6d1Z7d2Z8d3Z9d4Z:d5Z;d6Z<d7Z=d8Z>d9Z?d:Z@d;ZAd<ZBd=ZCd>ZDd?ZEd@ZFdAZGdBZHdCZIdDZJdEZKdFZLdGZMdHZNdIZOdJZPG dKdL dLeZQeMeQdMgdNdOdPiZRdQZSdRZTdSZUdTZVdUZWd@ZXdVZYdWZZdXZ[g dYZ\dS )Zz:Commonly-used constants which have not yet been organized.    N)
NamedTupleZbarcodesZtranslationZspZscZmmZANZCRZCBZCYZURZUBZUYZTXZGXZREfrZfxZxfZconf_mappedZconf_mapped_barcodedZconf_mapped_deduped_barcodedinsertfragmentZcdnaZall_bcsZfiltered_bcsZtranscriptomeZexonicZ
intergenicZintronicZcdna_pcrZontargetZ	offtarget   +   -Zthree_primeZ
five_primei  2      i        Zbc_sequenceZcellranger_versionzreference.jsonstarzfasta/genome.fazgenes/genes.gtfgenomesmem_gb
fasta_hashgtf_hashZinput_fasta_filesZinput_gtf_filesmkref_versionversiontypeZTranscriptomeZ
reference_g      ?   @   i Zb   ZnoneZ
library_idZmolecule_h5ZbatchdescriptionZcloupe_filec                   @   s*   e Zd ZU ee ed< eed< eed< dS )
aggr_filespathsrequireddefault_locationN)__name__
__module____qualname__liststr__annotations__bool r#   r#   c/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/python/cellranger/constants.pyr      s   
 r   zmolecule_info.h5T )r   r   r   i  Zvdjcounts
   NO_BARCODEz#E84B50g      ?)   C   z   z#1D437A)NonezNon-TargetingIgnore)]__doc__ostypingr   pathjoindirname__file__ZBARCODE_WHITELIST_PATHZ BARCODE_WHITELIST_TRANSLATE_PATHZSPATIAL_PRODUCT_TYPEZSINGLE_CELL_PRODUCT_TYPEZMULTIMAPPER_TAGZANTISENSE_TAGZRAW_BARCODE_TAGZPROCESSED_BARCODE_TAGZRAW_BARCODE_QUAL_TAGZRAW_UMI_TAGZPROCESSED_UMI_TAGZUMI_QUAL_TAGZTRANSCRIPTS_TAGZGENE_IDS_TAGZMAPPING_REGION_TAGZRAW_FEATURE_BARCODE_TAGZFEATURE_IDS_TAGZEXTRA_FLAGS_TAGZCONF_MAPPED_READ_TYPEZCONF_MAPPED_BC_READ_TYPEZCONF_MAPPED_DEDUPED_READ_TYPEZINSERT_MOLECULE_TYPEZFRAGMENT_MOLECULE_TYPEZCDNA_MOLECULE_TYPEZALL_BARCODESZFILTERED_BARCODESZTRANSCRIPTOME_REGIONZEXONIC_REGIONZINTERGENIC_REGIONZINTRONIC_REGIONZCDNA_PCR_DUPE_TYPEZON_TARGET_SUBSAMPLEZOFF_TARGET_SUBSAMPLEZFORWARD_STRANDZREVERSE_STRANDZSTRANDSZTHREE_PRIMEZ
FIVE_PRIMEr   rangeZINSERT_SIZE_CUTOFFSZMIN_COUNTS_PER_GENEZ%DEFAULT_RECOVERED_CELLS_PER_GEM_GROUPZTOP_NZHOMOPOLYMER_LENGTHZH5_BC_SEQUENCE_COLZCELLRANGER_VERSION_KEYREFERENCE_METADATA_FILEREFERENCE_STAR_PATHREFERENCE_FASTA_PATHREFERENCE_GENES_GTF_PATHREFERENCE_GENOMES_KEYREFERENCE_MEM_GB_KEYREFERENCE_FASTA_HASH_KEYREFERENCE_GTF_HASH_KEYREFERENCE_INPUT_FASTA_KEYREFERENCE_INPUT_GTF_KEYREFERENCE_MKREF_VERSION_KEYREFERENCE_VERSION_KEYZREFERENCE_TYPE_KEYZREFERENCE_TYPEZREFERENCE_METRIC_PREFIXZBAM_CHUNK_SIZE_GBZMAX_BAM_CHUNKSZCOUNT_GENES_MAX_MEM_GBZ#NUM_MOLECULE_INFO_ENTRIES_PER_CHUNKZSTAR_DEFAULT_HIGH_CONF_MAPQZNORM_MODE_NONEZAGG_ID_FIELDZAGG_H5_FIELDZAGG_BATCH_FIELDZAGG_DESCRIPTION_FIELDZAGG_CLOUPE_FIELDr   ZSC_AGGR_FILESZMAX_INSERT_SIZEZPIPELINE_VDJZPIPELINE_COUNTZ
NO_BARCODEZTISSUE_COLORZTISSUE_SPOTS_ALPHAZTISSUE_NOSPOTS_ALPHAZTISSUE_BBOX_COLORZFIDUCIAL_SPOT_COLORZFILTER_LISTr#   r#   r#   r$   <module>   s   