Mercurial > repos > geert-vandeweyer > coverage_report

comparison CoverageReport.pl @ 3:39c374d4cba7 draft

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Uploaded
author geert-vandeweyer
date Thu, 13 Feb 2014 04:45:48 -0500
parents 864d0ccfbe6f
children 2936bcb2a378
comparison
equal deleted inserted replaced
2:a9555d172896 3:39c374d4cba7
233 } 233 }
234 } 234 }
235 $avg = $sum/$counter; 235 $avg = $sum/$counter;
236 close IN; 236 close IN;
237 open OUT, ">$wd/Rout/hist.txt"; 237 open OUT, ">$wd/Rout/hist.txt";
238 if (!defined($dens{'0'})) {
239 $dens{'0'} = 0;
240 }
238 foreach (keys(%dens)) { 241 foreach (keys(%dens)) {
239 print OUT "$_;$dens{$_}\n"; 242 print OUT "$_;$dens{$_}\n";
240 } 243 }
241 close OUT; 244 close OUT;
242 if (!defined($dens{'0'})) {
243 $dens{'0'} = 0;
244 }
245 open OUT, ">$wd/Rout/ntplot.R"; 245 open OUT, ">$wd/Rout/ntplot.R";
246 # read coverage hist in R to plot 246 # read coverage hist in R to plot
247 print OUT 'coverage <- read.table("hist.txt" , as.is = TRUE, header=FALSE,sep=";")'."\n"; 247 print OUT 'coverage <- read.table("hist.txt" , as.is = TRUE, header=FALSE,sep=";")'."\n";
248 print OUT 'mincov <- '."$thresh \n"; 248 print OUT 'mincov <- '."$thresh \n";
249 print OUT "avg <- round($avg)\n"; 249 print OUT "avg <- round($avg)\n";