DUf ddlZddlZddlmZddlmZddlZejejddedej d d d ed ej dde ddej dddej dde ddej dddd ej ddedd ej dddde d!Z dS)"N)cli)api cool_path COOL_PATH)metavartypenargsz--outputz-oz?Specify output file name to store the coverage in a tsv format.F)helpr requiredz--ignore-diagszjThe number of diagonals to ignore. By default, equals the number of diagonals ignored during IC balancing.T)r r default show_defaultz--storezAppend columns with coverage (cov_cis_raw, cov_tot_raw), or (cov_cis_clr_weight_name, cov_tot_clr_weight_name) if calculating balanced coverage, to the cooler bin table. If clr_weight_name=None, also stores total cis counts in the cooler info)r is_flagz --chunksizezsSplit the contact matrix pixel records into equally sized chunks to save memory and/or parallelize. Default is 10^7gcAz--bigwigz`Also save output as bigWig files for cis and total coverage with the names ..bw)r rrz--clr_weight_namezLName of the weight column. Specify to calculate coverage of balanced cooler.z-pz--nproczQNumber of processes to split the work between. [default: 1, i.e. no process pool])r rr c"tj|}tj||||||\} } |ddgd} |Kddg} | t | | d<| t | | d<nPd|d |g} | t| | d<| t| | d<|r| |d d d n%t| d d d |rNtj | |j |d| dtj | |j |d| ddSdS)au Calculate the sums of cis and genome-wide contacts (aka coverage aka marginals) for a sparse Hi-C contact map in Cooler HDF5 format. Note that the sum(tot_cov) from this function is two times the number of reads contributing to the cooler, as each side contributes to the coverage. COOL_PATH : The paths to a .cool file with a balanced Hi-C map. ) ignore_diags chunksizenprocstoreclr_weight_nameN)chromstartend cov_cis_raw cov_tot_rawrrcov_cis_cov_tot_ Fnan)sepindexna_repz.cis.bw) value_fieldz.tot.bw) coolerCoolerrcoveragebinsastypeintfloatto_csvprintbioframe to_bigwig chromsizes) routputrrrbigwigrrclrcis_covtot_covcoverage_table store_namess S/var/www/html/software/conda/lib/python3.11/site-packages/cooltools/cli/coverage.pyr&r& sN - " "C|,, ,)5PUgv-GW XXZZ]#<#<#<=N$m4 )0)<)<{1~&)0)<)<{1~&&3/335Q5Q5QR )0)>)>{1~&)0)>)>{1~&Jf$eEJJJJ n##E%#HHIII    N   #A       N   #A          ) clickr$rrr-commandargumentstroptionr)r&r8r7r@s  3a J   <    7   7   ,        * 2 2 t2 2 2 r8