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paired-endÚsinglez
mate-pairszhq-mate-pairs)ÚpeÚsÚmpZhqmpZpacbioZsangerZnanoporeztrusted-contigszuntrusted-contigszfl-rnazassembly-graphÚecÚasÚmcZsccZtppzcontigs.fastazscaffolds.fastazraw_scaffolds.fastazassembly_graph.fastgz!assembly_graph_with_scaffolds.gfazcontigs.pathszraw_contigs.fastazscaffolds.pathszraw_scaffolds.pathsztranscripts.fastaztranscripts.pathsZhardZsoftzhmm_statistics.txtzgene_clusters.fastazdomain_graph.dotZpipeline_stateZbiosynthetic_spades_hmmsÚcoronaspades_hmmsé   é   é   é7   é-   é   é
   é   é   éú   é!   é1   éM   éc   ÚtmpZread_conversionZlastc             C   s"   d| |f }t jjtjt|ƒ}|S )Nzstage_%d_%s)ÚosÚpathÚjoinÚargsÚ
output_dirÚpipeline_state_dir)Z	stage_numZstage_short_nameZstage_file_nameZstage_checkpoint_path© r    úe/home/psgendb/BIRCHDEV/pkg/SPAdes-3.15.4/linux-x86_64/share/spades/spades_pipeline/options_storage.pyÚget_stage_filename`   s    r"   c               C   s(   t j o&t j o&t j o&t jo$t j  S )N)r   Zk_mersÚsingle_cellÚ
iontorrentÚmetaÚplasmidr    r    r    r!   Úauto_K_allowedg   s    r'   c               C   s   t jpt jpt jS )N)r   ÚbioÚcustom_hmmsÚcoronar    r    r    r!   Úhmm_modej   s    r+   )Br   Zoriginal_k_mersÚdictÚdict_of_prefixesÚdict_of_rel2absZcorrect_scaffoldsZrun_truseq_postprocessingÚSUPPORTED_PYTHON_VERSIONSÚBH_ALLOWED_READS_EXTENSIONSÚ(IONTORRENT_ONLY_ALLOWED_READS_EXTENSIONSÚ CONTIGS_ALLOWED_READS_EXTENSIONSÚGRAPH_ALLOWED_READS_EXTENSIONSÚALLOWED_READS_EXTENSIONSZMAX_LIBS_NUMBERZOLD_STYLE_READS_OPTIONSÚSHORT_READS_TYPESÚLONG_READS_TYPESÚGRAPH_READS_TYPESZSHORT_STAGES_NAMEÚcontigs_nameÚscaffolds_nameÚsecondary_scaffolds_nameÚassembly_graph_nameÚassembly_graph_name_gfaÚcontigs_pathsÚsecondary_contigs_nameÚscaffolds_pathsÚsecondary_scaffolds_pathsÚtranscripts_nameÚtranscripts_pathsÚfiltering_typesÚbgc_stats_nameZgene_clusters_nameÚdomain_graph_namer   Zbiosyntheticspades_hmmsr
   ZMIN_KZMAX_KZ	RNA_MIN_KZRNA_MAX_LOWER_KZRNA_VIRAL_MAX_LOWER_KZ THRESHOLD_FOR_BREAKING_SCAFFOLDSZ)THRESHOLD_FOR_BREAKING_ADDITIONAL_CONTIGSZGAP_CLOSER_ENABLE_MIN_KZSCC_KZTHREADSZMEMORYZ
K_MERS_RNAZK_MERS_SHORTZ
K_MERS_150Z
K_MERS_250ZK_MERS_PLASMID_100ZK_MERS_PLASMID_LONGZ
ITERATIONSZTMP_DIRÚ READS_TYPES_USED_IN_CONSTRUCTIONZREADS_TYPES_USED_IN_RNA_SEQÚ
BASE_STAGEÚ
LAST_STAGEÚfirst_command_liner   Zoriginal_dataset_datar"   r'   r+   r    r    r    r!   Ú<module>
   s€   
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