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 d g Z d	 d
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 e Z d Z d d d d d g Z i d d 6d d 6d d 6d d 6d d 6Z d d d d d  d! d" g Z d# d$ d% d& d' g Z d( Z d) Z d* Z d+ Z d, Z d- Z d. Z d/ Z d0 d1 d2 g Z d3 Z d4 Z d5 Z d6 Z d7 Z  d8 Z! d9 Z" d: Z# d; Z$ d< Z% d= Z& d; Z' d> Z( d? Z) d@ Z* dA dB g Z+ d> dA d; g Z, d> dA d; dC g Z- d> dA d; dC dD d9 g Z. d> dA d; dC g Z/ d> dA d; dC dD d9 g Z0 d8 Z1 dE Z2 d d d g Z3 d d d  d! d d d" g Z4 dF Z5 dG Z6 d Z7 d Z8 dH „  Z9 dI „  Z: d S(J   iÿÿÿÿNs   2.7s   3.2+s   .fqs   .fastqs   .bams   .fq.gzs	   .fastq.gzs   .fas   .fastas   .fa.gzs	   .fasta.gzi	   s   --12s   -1s   -2s   -ss   --mergeds
   paired-endt   pet   singlet   ss
   mate-pairst   mps   hq-mate-pairst   hqmpt   nxmatet   pacbiot   sangert   nanoporet   tslrs   trusted-contigss   untrusted-contigss   fl-rnat   ect   ast   mct   scct   tpps   contigs.fastas   scaffolds.fastas   assembly_graph.fastgs!   assembly_graph_with_scaffolds.gfas   contigs.pathss   scaffolds.pathss   transcripts.fastas   transcripts.pathst   hardt   softt   defaults   bgc_statistics.txts   gene_clusters.fastas   domain_graph.dott   pipeline_statet   biosynthetic_spades_hmmsi   i   i   i7   i   i
   i   i   iú   i!   i1   iM   ic   t   tmpt   read_conversiont   lastc         C   s/   d |  | f } t  j j t j t | ƒ } | S(   Ns   stage_%d_%s(   t   ost   patht   joint   argst
   output_dirt   pipeline_state_dir(   t	   stage_numt   stage_short_namet   stage_file_namet   stage_checkpoint_path(    (    ss   /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.14.0-Linux/share/spades/spades_pipeline/options_storage.pyt   get_stage_filenameX   s    c           C   s0   t  j o/ t  j o/ t  j o/ t  j o. t  j S(   N(   R   t   k_merst   single_cellt
   iontorrentt   metat   plasmid(    (    (    ss   /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.14.0-Linux/share/spades/spades_pipeline/options_storage.pyt   auto_K_allowed_   s    (;   R   t   Nonet   original_k_merst   dictt   dict_of_prefixest   dict_of_rel2abst   Falset   correct_scaffoldst   run_truseq_postprocessingt   SUPPORTED_PYTHON_VERSIONSt   BH_ALLOWED_READS_EXTENSIONSt(   IONTORRENT_ONLY_ALLOWED_READS_EXTENSIONSt    CONTIGS_ALLOWED_READS_EXTENSIONSt   ALLOWED_READS_EXTENSIONSt   MAX_LIBS_NUMBERt   OLD_STYLE_READS_OPTIONSt   SHORT_READS_TYPESt   LONG_READS_TYPESt   SHORT_STAGES_NAMEt   contigs_namet   scaffolds_namet   assembly_graph_namet   assembly_graph_name_gfat   contigs_pathst   scaffolds_pathst   transcripts_namet   transcripts_pathst   filtering_typest   bgc_stats_namet   gene_clusters_namet   domain_graph_nameR   t   biosyntheticspades_hmmst   MIN_Kt   MAX_Kt	   RNA_MIN_Kt   RNA_MAX_LOWER_Kt    THRESHOLD_FOR_BREAKING_SCAFFOLDSt)   THRESHOLD_FOR_BREAKING_ADDITIONAL_CONTIGSt   GAP_CLOSER_ENABLE_MIN_Kt   SCC_Kt   THREADSt   MEMORYt
   K_MERS_RNAt   K_MERS_SHORTt
   K_MERS_150t
   K_MERS_250t   K_MERS_PLASMID_100t   K_MERS_PLASMID_LONGt
   ITERATIONSt   TMP_DIRt    READS_TYPES_USED_IN_CONSTRUCTIONt   READS_TYPES_USED_IN_RNA_SEQt
   BASE_STAGEt
   LAST_STAGEt   first_command_lineR   R!   R'   (    (    (    ss   /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.14.0-Linux/share/spades/spades_pipeline/options_storage.pyt   <module>
   sn   			
)	