Use of read names to determine input file type

[aleferna]

getftype uses the read names to determine the file type ( 0 == fastq, 1 == fasta and 2 == sam). In practice read names should be considered free text and I think you should prabably get the file type from the extension or ask the user as a parameter. In our case since we do not use this read naming scheme it was detecting our input as fasta even though it was fastq and this lead to interger overruns.