
    DUf                        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n# e	$ r dZY nw xY wd dl
mZ i ddd	d
dddddddddddddddddddddd d!d"d#d$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sDe                                D ]"\  ZZe\  ZZ edYee           e            e<   # ee          ZdS  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<   dS )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                 $    t          d| |          S )Nsamtoolsr	   )r:   r;   s     K/var/www/html/software/conda/lib/python3.11/site-packages/pysam/samtools.py_wrap_commandr@   E   s     :x999    r>      r.   r7   r/   r0   r1   r2   r3   r4   r8   r9   r6   )Eplatformtypingr   r   r   r   r   r   
HAVE_FINALImportErrorpysam.utilsr
   _SAMTOOLS_DISPATCHstrr@   itemskeyoptionscmdparserglobalslist__all__r   __annotations__r   r   r   r   r   r   r   r   r   r   r   r   r   r   r   r   r   r   r   r    r!   r"   r#   r$   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                JJ   JJJ ( ' ' ' ' '/
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[: : : : :  yx*0022 B BWV(S&AA		#d%&&GGG $1=1CF1KA1NPbciPjklPm#n#nD%
 nnn#0=1CF1KA1NPbciPjklPm#n#nD%
 nnn#0=1CF1KA1NPbciPjklPm#n#nD%
 nnn&3m4Fy4QRS4TVhirVstuVv&w&wGU?#www(5;'*;'*) )Iu_%   
 %2M2DW2Ma2PRdelRmnoRp$q$qE5!qqq$1M2DW2Ma2PRdelRmnoRp$q$qE5!qqq$1M2DW2Ma2PRdelRmnoRp$q$qE5!qqq$1M2DW2Ma2PRdelRmnoRp$q$qE5!qqq$1M2DW2Ma2PRdelRmnoRp$q$qE5!qqq'4}5G
5STU5VXjkuXvwxXy'z'zHeO$zzz&3m4Fy4QRS4TVhirVstuVv&w&wGU?#www'4}5G
5STU5VXjkuXvwxXy'z'zHeO$zzz$1M2DW2Ma2PRdelRmnoRp$q$qE5!qqq$1M2DW2Ma2PRdelRmnoRp$q$qE5!qqq&3m4Fy4QRS4TVhirVstuVv&w&wGU?#www$1M2DW2Ma2PRdelRmnoRp$q$qE5!qqq(5;'*;'*) )Iu_%   
 (5}5G
5STU5VXjkuXvwxXy'z'zHeO$zzz$1M2DW2Ma2PRdelRmnoRp$q$qE5!qqq"/-0B50I!0LN`afNghiNj"k"kC	kkk(5;'*;'*) )Iu_%   
 %2M2DW2Ma2PRdelRmnoRp$q$qE5!qqq%2]3Eh3OPQ3RTfgoTpqrTs%t%tFE/"ttt#0=1CF1KA1NPbciPjklPm#n#nD%
 nnn+8=>*1->*1-, ,L%(   
 )6;'*;'*) )Iu_%   
 %2M2DW2Ma2PRdelRmnoRp$q$qE5!qqq%2]3Eh3OPQ3RTfgoTpqrTs%t%tFE/"ttt'4}5G
5STU5VXjkuXvwxXy'z'zHeO$zzz&3m4Fy4QRS4TVhirVstuVv&w&wGU?#www&3m4Fy4QRS4TVhirVstuVv&w&wGU?#www$1M2DW2Ma2PRdelRmnoRp$q$qE5!qqq$1M2DW2Ma2PRdelRmnoRp$q$qE5!qqq$1M2DW2Ma2PRdelRmnoRp$q$qE5!qqq(56H6UVW6XZlmxZyz{Z|(}(}Iu_%}}})6<(+<(+* *Jo&   
 %2M2DW2Ma2PRdelRmnoRp$q$qE5!qqq$1M2DW2Ma2PRdelRmnoRp$q$qE5!qqq+8=>*1->*1-, ,L%(   
 -:M?+A.?+A.- -M5)   
 '4m4Fy4QRS4TVhirVstuVv&w&wGU?#www'4}5G
5STU5VXjkuXvwxXy'z'zHeO$zzz&3m4Fy4QRS4TVhirVstuVv&w&wGU?#www&3m4Fy4QRS4TVhirVstuVv&w&wGU?#wwwwws    ((