fixed for reads longer than 100n

dge_workflow/fastqc_summary.R

@@ -17,7 +17,6 @@ argv = commandArgs(TRUE)
 
 if(length(argv) != 1){
     stop("Usage: fastqc_summmary.R <directory with fastqc results>")
-    echo
 }
 
 baseDir=argv[1]
@@ -111,7 +110,7 @@ readBaseQualDist <- function(statsFile){
 #    echo("reading", statsFile)
 
     baseStats <- read.delim(pipe(
-            paste(get_zip_pipe(statsFile, "fastqc_data.txt"), " | grep -A50 -F '>>Per base sequence quality' | grep -B100 -F '>>END_MODULE' | head -n-1 | tail -n+2 | tr '#' ' '")
+            paste(get_zip_pipe(statsFile, "fastqc_data.txt"), " | grep -A60 -F '>>Per base sequence quality' | grep -B100 -F '>>END_MODULE' | head -n-1 | tail -n+2 | tr '#' ' '")
         )) %>% mutate(
             run=trim_ext(basename(statsFile), c(".zip"))
         )
@@ -120,7 +119,7 @@ readBaseQualDist <- function(statsFile){
 }
 
 baseQualities <- fastqDataFiles %>%  ldply(readBaseQualDist)
-
+statsFile="fastqc/L8038_Track-21511_R1.trim_fastqc.zip"
 #with(baseQualities, as.data.frame(table(run)))