De/Compressor detection will not work properly in all cases

[dankwart-de]

The current detection code is:

      for (int i = 0; i < er.resultLines.size(); i++) {
            //Look at Matthias ExomePipeline extension. The code is mainly taken from there.
            String dCString = null
            String dRString = "gzip -c" //POSSIBLE-ERROR: Not zipper set for 'cat'/ASCII
            String type = er.resultLines[i]
            if (type.startsWith("setgid "))
                type = type[7..-1].trim().split(" ")[0]
            if (type == "0") continue
            if (type == "gzip") {
                dCString = "gunzip -c"
                dRString = "gzip -c"
            } else if (type == "bzip2") {
                dCString = "bunzip2 -c -k"
                dRString = "bzip2 -c -k"
            } else if (type == "ASCII" || type == "ASCII text") {
                dCString = "cat"
                dRString = "head -n E"
            }
            allLaneFiles[i].setDecompressionString(dCString)
            allLaneFiles[i].setRecompressionString(dRString)
        }

file -bL used to work? (or we did not recognize that it never worked properly due to other circumstances). It needs to recognize strings e.g. from:

ASCII text with very long lines

[vinjana]

What do you mean, it needs to recognize strings? Can you add a test file where it fails and the desired outcome?