
    tfg                        d dl Z d dlZd dl d dlmZ d dl d dl d dl d dlmZ d dlm	Z	 d dl d dl
mZ d dl
 d dlmZ d dl d dlmZ d dl d dlmZ d dl d dlmZ d dl d dlmZ d dl d dlmZ d dl d dlmZ d dl d dlmZ d dlmZ d dl d dlZ ejB                  ejB                  z   ejB                  z   ejB                  z   ejB                  z   ejB                  z   e	jB                  z   ejB                  z   ejB                  z   ejB                  z   ejB                  z   dgz   dgz   Z!d dl"m#Z#m$Z$ d Z%d Z&d	 Z'y)
    N)*)SamtoolsErrorr   Pileup)__version____samtools_version__c                     t         j                  j                  t         j                  j                  t         j                  j	                  t
                          } t         j                  j                  | dd      t         j                  j                  | dd      g}t         j                  j                  | dd      t         j                  j                  | dd      g}| g}||fD ]X  }|D ]Q  }t         j                  j                  |      s#|j                  t         j                  j                  |              X Z |S )z%return a list of include directories.z..htslibincludesamtools)ospathabspathjoindirname__file__existsappend)r   htslib_possibilitiessamtool_possibilitiesincludesheader_locationsheader_locations         X/var/www/html/software/conda/envs/higlass/lib/python3.12/site-packages/pysam/__init__.pyget_includer   5   s    ggoobggll277??8+DEFG GGLL$AGGLL)XFHWW\\'4DWW\\'9jIK yH13HI / 	Oww~~o. @A	 O    c                      g S )z0return a list of defined compilation parameters. r   r   r   get_definesr   N   s	     Ir   c                     t         j                  j                  t         j                  j                  t         j                  j	                  t
                          } g d}t        j                  j                  dk(  r|j                  d       t        j                  d      }|D cg c]%  }t         j                  j                  | ||z         ' c}S c c}w )z+return a list of libraries to link against.)libctabixproxies	libcfaidxlibcsamfilelibcvcflibcbcf	libctabixbuiltin
libchtslib
EXT_SUFFIX)r   r   r   r   r   r   pysamconfigHTSLIBr   	sysconfigget_config_var)r   
pysam_libssoxs       r   get_librariesr1   U   s     ggoobggll277??8+DEFGJ ||i','		!	!,	/B3=>aBGGLL!b&)>>>s   )*C)(r   r,   pysam.libchtslibr'   pysam.libcsamtoolspysam.libcbcftoolspysam.libcutils	libcutilspysam.libcfaidxr!   pysam.libctabixr%   pysam.libctabixproxiesr    pysam.libcsamfiler"   pysam.libcalignmentfilelibcalignmentfilepysam.libcalignedsegmentlibcalignedsegmentpysam.libcvcfr#   pysam.libcbcfr$   pysam.libcbgzflibcbgzfpysam.utilsr   pysam.Pileupr   pysam.samtoolspysam.configr)   __all__pysam.versionr   r   r   r   r1   r   r   r   <module>rI      s4   	   %      # #  #  1 $ '  3 % 5 &     !  %   
  OO OO	
     	 
  J  <2?r   