dvera / harp Goto Github PK

Hi,
:
I am trying to parse mouse haplotypes but I am confronted by this error:

library(harp)

f <- file("*.fastq")
ref1 <- "/path/to/C57BL_6NJ"
ref2 <- "/path/to/CAST_EiJ"
harp( f, index1prefix=ref1, index2prefix=ref2 )
Error in removeext(fastqFiles1) : could not find function "removeext"

any idea what i'm doing wrong?

Thanks

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

I want to use the HARP algorithm to pick apart reads from your published replication timing. After installing everything I am able to import the harp package. However, when trying to call the function

harp(f, index1prefix=/path index2prefix=/path)

I get an error saying it cannot find the function

Error: object 'harp' not found

I had a look at the NAMESPACE file and the rscript and there seem to be roxygen2 directives missing which prevent the package from exporting the contained function.