ó
XgÃac           @   sŒ  d  d l  Z  d Z e ƒ  Z e ƒ  Z e Z e Z d d g Z	 d d d d d g Z
 d g Z d	 d
 d d g Z d g Z e
 e e Z d Z d d d d d g Z i d d 6d d 6d d 6d d 6Z d d d d d  d! g Z d" g Z d# d$ d% d& d' g Z d( Z d) Z d* Z d+ Z d, Z d- Z d. Z d/ Z d0 Z d1 Z d2 Z d3 d4 g Z  d5 Z! d6 Z" d7 Z# d8 Z$ d9 Z% d: Z& d; Z' d< Z( d= Z) d> Z* d? Z+ d@ Z, dA Z- d> Z. dB Z/ dC Z0 dD Z1 dE dF g Z2 dB dE d> g Z3 dB dE d> dG g Z4 dB dE d> dG dH d< g Z5 dB dE d> dG g Z6 dB dE d> dG dH d< g Z7 d; Z8 dI Z9 d d d g Z: d d d d  d d d! g Z; dJ Z< dK Z= d Z> d Z? d Z@ dL „  ZA dM „  ZB dN „  ZC d S(O   iÿÿÿÿNs   2.7s   3.2+s   .fqs   .fastqs   .bams   .fq.gzs	   .fastq.gzs   .fas   .fastas   .fa.gzs	   .fasta.gzs   .gfai	   s   --12s   -1s   -2s   -ss   --mergeds
   paired-endt   pet   singlet   ss
   mate-pairst   mps   hq-mate-pairst   hqmpt   pacbiot   sangert   nanopores   trusted-contigss   untrusted-contigss   fl-rnas   assembly-grapht   ect   ast   mct   scct   tpps   contigs.fastas   scaffolds.fastas   raw_scaffolds.fastas   assembly_graph.fastgs!   assembly_graph_with_scaffolds.gfas   contigs.pathss   raw_contigs.fastas   scaffolds.pathss   raw_scaffolds.pathss   transcripts.fastas   transcripts.pathst   hardt   softs   hmm_statistics.txts   gene_clusters.fastas   domain_graph.dott   pipeline_statet   biosynthetic_spades_hmmst   coronaspades_hmmsi   i   i   i7   i-   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-3.15.4-Linux/share/spades/spades_pipeline/options_storage.pyt   get_stage_filename`   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-3.15.4-Linux/share/spades/spades_pipeline/options_storage.pyt   auto_K_allowedg   s    c           C   s   t  j p t  j p t  j S(   N(   R   t   biot   custom_hmmst   corona(    (    (    ss   /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.15.4-Linux/share/spades/spades_pipeline/options_storage.pyt   hmm_modej   s    (D   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   GRAPH_ALLOWED_READS_EXTENSIONSt   ALLOWED_READS_EXTENSIONSt   MAX_LIBS_NUMBERt   OLD_STYLE_READS_OPTIONSt   SHORT_READS_TYPESt   LONG_READS_TYPESt   GRAPH_READS_TYPESt   SHORT_STAGES_NAMEt   contigs_namet   scaffolds_namet   secondary_scaffolds_namet   assembly_graph_namet   assembly_graph_name_gfat   contigs_pathst   secondary_contigs_namet   scaffolds_pathst   secondary_scaffolds_pathst   transcripts_namet   transcripts_pathst   filtering_typest   bgc_stats_namet   gene_clusters_namet   domain_graph_nameR   t   biosyntheticspades_hmmsR   t   MIN_Kt   MAX_Kt	   RNA_MIN_Kt   RNA_MAX_LOWER_Kt   RNA_VIRAL_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   t   original_dataset_dataR   R%   R)   (    (    (    ss   /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.15.4-Linux/share/spades/spades_pipeline/options_storage.pyt   <module>
   s€   				"			