harp throws an error with single-end reads

[dmalzl]

I course of resolving #1 I simply copied the code for the function into my script and loaded conifur, gyro, converge and travis manually in addition. However, when using single-end files the function throws an error resulting from the undefined variable paired when calling bowtie2 in line 88. This is due to the fact that if fastqFiles2 is not given (hence NULL) the preceeding if statement is not called and paired is not set. Putting

  if(!sam){
    if(!is.null(fastqFiles2)){
      paired=TRUE
    } else{
      paired=FALSE
    }
    sam1 <- bowtie2(fastqFiles1, index1prefix, if(paired){fastqFiles2}, discordant=TRUE, appendIndexToName=TRUE, reorder=TRUE, threads=threads )
    sam2 <- bowtie2(fastqFiles1, index2prefix, if(paired){fastqFiles2}, discordant=TRUE, appendIndexToName=TRUE, reorder=TRUE, threads=threads )
  }

reolves the problem

[dvera]

Sorry for the delay, I didn't get notified of the issue. Should be fixed now.