
    kVf                     J   U d dl Z d dlmZmZmZmZmZ 	 d dlmZ dZd dl
mZ i ddd	d
dddddddddddddddddddddd d!d"d#d$d%d&d'd(i d)d*d+d,d-d.d/d0d1d2d3d4d5d6d7d8d9d:d;d<d=d<d>d?d@dAdBdCdDdEdFdGdHdIdJdKdLdMdNdOdPdQdRdRdSdTZdUedVeeeeeeee   f   geeee   f   f   f      dWefdXZes8ej                         D ]  \  ZZe\  ZZ edYee       e       e<     ee      Zy eed   d    ed   dZ         Zee   ed<    eed	   d    ed	   dZ         Zee   ed	<    eed   d    ed   dZ         Zee   ed<    eed   d    ed   dZ         Zee   ed<    eed   d    ed   dZ         Zee   ed<    eed   d    ed   dZ         Zee   ed<    eed   d    ed   dZ         Zee   ed<    eed   d    ed   dZ         Zee   ed<    eed   d    ed   dZ         Z ee   ed<    eed   d    ed   dZ         Z!ee   ed<    eed   d    ed   dZ         Z"ee   ed<    eed   d    ed   dZ         Z#ee   ed<    eed   d    ed   dZ         Z$ee   ed<    eed!   d    ed!   dZ         Z%ee   ed!<    eed#   d    ed#   dZ         Z&ee   ed#<    eed%   d    ed%   dZ         Z'ee   ed%<    eed'   d    ed'   dZ         Z(ee   ed'<    eed)   d    ed)   dZ         Z)ee   ed)<    eed+   d    ed+   dZ         Z*ee   ed+<    eed-   d    ed-   dZ         Z+ee   ed-<    eed/   d    ed/   dZ         Z,ee   ed/<    eed1   d    ed1   dZ         Z-ee   ed1<    eed3   d    ed3   dZ         Z.ee   ed3<    eed5   d    ed5   dZ         Z/ee   ed5<    eed7   d    ed7   dZ         Z0ee   ed7<    eed9   d    ed9   dZ         Z1ee   ed9<    eed;   d    ed;   dZ         Z2ee   ed;<    eed=   d    ed=   dZ         Z3ee   ed=<    eed>   d    ed>   dZ         Z4ee   ed><    eed@   d    ed@   dZ         Z5ee   ed@<    eedB   d    edB   dZ         Z6ee   edB<    eedD   d    edD   dZ         Z7ee   edD<    eedF   d    edF   dZ         Z8ee   edF<    eedH   d    edH   dZ         Z9ee   edH<    eed[   d    ed[   dZ         Z:ee   ed[<    eed\   d    ed\   dZ         Z;ee   ed\<    eed]   d    ed]   dZ         Z<ee   ed]<    eed^   d    ed^   dZ         Z=ee   ed^<    eed_   d    ed_   dZ         Z>ee   ed_<    eed`   d    ed`   dZ         Z?ee   ed`<    eeda   d    eda   dZ         Z@ee   eda<    eedb   d    edb   dZ         ZAee   edb<    eedc   d    edc   dZ         ZBee   edc<    eedd   d    edd   dZ         ZCee   edd<    eede   d    ede   dZ         ZDee   ede<   y# e	$ r dZY w xY w)f    N)CallableListTupleIterableUnion)FinalTFPysamDispatcherview)r    head)r   r   sort)r   r   mpileup)r   r   	consensus)r   r   depth)r   r   faidx)r   r   fqidx)r   r   tview)r   r   index)r   r   idxstats)r   r   fixmate)r   r   flagstat)r   r   calmd)r   r   merge)r   r   markdup)r   r   rmdup)r   r   	reference)r   r   reheader)r   r   reset)r   r   cat)r    r   	targetcut)r!   r   phase)r"   r   bam2fq)r#   r   dict)r$   r   addreplacerg)r%   r   	pad2unpad)r&   r   depadbedcov)r(   r   coverage)r)   r   bamshuf)r*   r   collate)r+   r   stats)r,   r   fasta)r-   r   )fastqr   )z	cram-sizer   )
quickcheckr   )splitr   )flagsr   )ampliconclipr   )ampliconstatsr   )versionr   )importr   )samplesr   )r.   	cram_sizer/   r0   r1   r2   r3   r4   fqimportimport_r6   dispatchparsersreturnc                     t        d| |      S )Nsamtoolsr	   )r:   r;   s     W/var/www/html/software/conda/envs/catlas/lib/python3.12/site-packages/pysam/samtools.py_wrap_commandr@   E   s     :x99    r>      r.   r7   r/   r0   r1   r2   r3   r4   r8   r9   r6   )Eplatformtypingr   r   r   r   r   r   
HAVE_FINALImportErrorpysam.utilsr
   _SAMTOOLS_DISPATCHstrr@   itemskeyoptionscmdparserglobalslist__all__r   __annotations__r   r   r   r   r   r   r   r   r   r   r   r   r   r   r   r   r   r   r   r    r!   r"   r#   r$   r%   r&   r'   r(   r)   r*   r+   r,   r-   r.   r7   r/   r0   r1   r2   r3   r4   r8   r9   r6   r   rA   r?   <module>rS      s    J (/
L/ L/ L	/
 / "/ ]/ ]/ ]/ ]/ ]/  / /  / ]/  ]!/" #/$ ]%/& "'/(  )/* ]+/, 
;-/. "//0 ]1/2 n3/4 L5/6 (7/8 "9/: ;/< n=/>  ?/@ A/B C/D ]E/F ]G/H "$(*]/ d::eC5d3i+@*A5dSViCX*X!YYZ[: : *002 BWV(S&A	#B %&G $11CF1KA1NPbciPjklPm#nD%
 n#01CF1KA1NPbciPjklPm#nD%
 n#01CF1KA1NPbciPjklPm#nD%
 n&34Fy4QRS4TVhirVstuVv&wGU?#w(5;'*;'*)Iu_% 
 %22DW2Ma2PRdelRmnoRp$qE5!q$12DW2Ma2PRdelRmnoRp$qE5!q$12DW2Ma2PRdelRmnoRp$qE5!q$12DW2Ma2PRdelRmnoRp$qE5!q$12DW2Ma2PRdelRmnoRp$qE5!q'45G
5STU5VXjkuXvwxXy'zHeO$z&34Fy4QRS4TVhirVstuVv&wGU?#w'45G
5STU5VXjkuXvwxXy'zHeO$z$12DW2Ma2PRdelRmnoRp$qE5!q$12DW2Ma2PRdelRmnoRp$qE5!q&34Fy4QRS4TVhirVstuVv&wGU?#w$12DW2Ma2PRdelRmnoRp$qE5!q(5;'*;'*)Iu_% 
 (55G
5STU5VXjkuXvwxXy'zHeO$z$12DW2Ma2PRdelRmnoRp$qE5!q"/0B50I!0LN`afNghiNj"kC	k(5;'*;'*)Iu_% 
 %22DW2Ma2PRdelRmnoRp$qE5!q%23Eh3OPQ3RTfgoTpqrTs%tFE/"t#01CF1KA1NPbciPjklPm#nD%
 n+8>*1->*1-,L%( 
 )6;'*;'*)Iu_% 
 %22DW2Ma2PRdelRmnoRp$qE5!q%23Eh3OPQ3RTfgoTpqrTs%tFE/"t'45G
5STU5VXjkuXvwxXy'zHeO$z&34Fy4QRS4TVhirVstuVv&wGU?#w&34Fy4QRS4TVhirVstuVv&wGU?#w$12DW2Ma2PRdelRmnoRp$qE5!q$12DW2Ma2PRdelRmnoRp$qE5!q$12DW2Ma2PRdelRmnoRp$qE5!q(56H6UVW6XZlmxZyz{Z|(}Iu_%})6<(+<(+*Jo& 
 %22DW2Ma2PRdelRmnoRp$qE5!q$12DW2Ma2PRdelRmnoRp$qE5!q+8>*1->*1-,L%( 
 -:?+A.?+A.-M5) 
 '44Fy4QRS4TVhirVstuVv&wGU?#w'45G
5STU5VXjkuXvwxXy'zHeO$z&34Fy4QRS4TVhirVstuVv&wGU?#w&34Fy4QRS4TVhirVstuVv&wGU?#ws  Js   X X"!X"