#NEWLINE# @ active_if ( ( 'idba' in ASSEMBLERS ) ) #NEWLINE# @ transform ( buildContigLengths , suffix ( '.lengths.tsv' ) , add_inputs ( mapReadsWithBowtieAgainstIdbaContigs ) , '.coverage' ) #NEWLINE# def buildCoverageOverIdbaContigs( infiles , outfile ) : #NEWLINE# #INDENT# '\n    build histograms of the coverage over each of the contigs\n    ' #NEWLINE# inf = ( infiles [ 0 ] . find ( 'idba' ) != ( - 1 ) ) #NEWLINE# if inf : #NEWLINE# #INDENT# size = infiles [ 0 ] #NEWLINE# bam = infiles [ 1 ] #NEWLINE# statement = 'bedtools genomecov -split -ibam %(bam)s -g %(size)s -d > %(outfile)s' #NEWLINE# P . run ( )